668 lines
14 KiB
C
Executable File
668 lines
14 KiB
C
Executable File
#include <stdio.h>
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#include <malloc.h>
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#include <strings.h>
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#include <xview/xview.h>
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#include <xview/scrollbar.h>
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#include <xview/panel.h>
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#include <xview/window.h>
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#include <xview/notice.h>
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#include <xview/textsw.h>
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#include "menudefs.h"
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#include "defines.h"
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/*
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Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory.
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All rights reserved.
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*/
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EditCut(item,event)
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Panel_item item;
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Event *event;
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{
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extern Frame frame;
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extern Canvas EditCan,EditNameCan;
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extern Panel_item left_foot,right_foot;
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extern NA_Alignment *DataSet,*Clipboard;
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char buffer[80];
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int j,numselected=0,numshifted = 0;
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if(TestSelection() == SELECT_REGION)
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return(EditSubCut(item,event));
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for(j=0;j<Clipboard->numelements;j++)
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{
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FreeNASeq(Clipboard->element[j]);
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InitNASeq(&(Clipboard->element[j]),TEXT);
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}
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Clipboard->numelements = 0;
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for(j=0;j<DataSet->numelements;j++)
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if(DataSet->element[j].selected)
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{
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if(numselected >= Clipboard->maxnumelements-1)
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{
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Clipboard->maxnumelements += 10;
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Clipboard->element = (NA_Sequence*)Realloc
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(Clipboard->element,
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Clipboard->maxnumelements*sizeof(NA_Sequence));
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}
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Clipboard->element[(Clipboard->numelements)] =
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DataSet->element[j];
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/*
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* Map sequences back into their global positions, as we will
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* normailze the alignment after they are copied out.
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*/
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Clipboard->element[(Clipboard->numelements)++].offset+=
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DataSet->rel_offset;
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numselected++;
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}
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for(j=0;j<DataSet->numelements;j++)
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if(DataSet->element[j].selected)
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numshifted++;
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else
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DataSet->element[j-numshifted] =
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DataSet->element[j];
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DataSet->numelements -= numshifted;
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NormalizeOffset(DataSet);
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SetNADData(DataSet,EditCan,EditNameCan);
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Regroup(DataSet);
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RepaintAll(TRUE);
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sprintf(buffer,"%d sequence in Sequence Clipboard",numselected);
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xv_set(frame,FRAME_RIGHT_FOOTER,buffer,0);
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xv_set(right_foot,PANEL_LABEL_STRING,buffer,0);
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return(XV_OK);
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}
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EditCopy(item,event)
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Panel_item item;
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Event *event;
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{
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extern Frame frame;
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extern Canvas EditCan,EditNameCan;
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extern NA_Alignment *DataSet,*Clipboard;
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extern Panel_item left_foot,right_foot;
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char buffer[80];
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int i,j,numselected=0,numshifted = 0,this;
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if(TestSelection() == SELECT_REGION)
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return(EditSubCopy(item,event));
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for(j=0;j<Clipboard->numelements;j++)
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{
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FreeNASeq(Clipboard->element[j]);
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InitNASeq(&(Clipboard->element[j]),TEXT);
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}
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Clipboard->numelements = 0;
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for(j=0;j<DataSet->numelements;j++)
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if(DataSet->element[j].selected)
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{
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this = Clipboard->numelements;
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if(numselected >= Clipboard->maxnumelements-1)
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{
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Clipboard->maxnumelements += 10;
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Clipboard->element = (NA_Sequence*)Realloc
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(Clipboard->element,
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Clipboard->maxnumelements*sizeof(NA_Sequence));
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InitNASeq(&(Clipboard->element
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[this]),
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DataSet->element[j].elementtype);
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}
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Clipboard->element[this] = DataSet->element[j];
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/*
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* Handle comments
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*/
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if(DataSet->element[j].comments)
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{
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Clipboard->element[this].comments = (char*)
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strdup(DataSet->element[j].comments);
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Clipboard->element[this].comments_maxlen =
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Clipboard->element[this].comments_len;
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}
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/*
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* And baggage
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*/
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if(DataSet->element[j].baggage)
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{
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Clipboard->element[this].baggage = (char*)
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strdup(DataSet->element[j].baggage);
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Clipboard->element[this].baggage_maxlen =
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Clipboard->element[this].baggage_len;
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}
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Clipboard->element[this].cmask = NULL;
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Clipboard->element[this].sequence
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= (NA_Base*)Calloc(DataSet->element[j].seqmaxlen,
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sizeof(NA_Base));
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for(i=0;i<DataSet->element[j].seqlen;i++)
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Clipboard->element[Clipboard->numelements].
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sequence[i] = DataSet->element[j].sequence[i];
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/*
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putelem(&(Clipboard->element[Clipboard->
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numelements]),i,
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getelem(&(DataSet->element[j]),i));
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*/
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/*
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* Map sequences back into their global positions, as we will
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* normailze the alignment after they are copied out.
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*/
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Clipboard->element[(Clipboard->numelements)].offset +=
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DataSet->rel_offset;
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(Clipboard->numelements)++;
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numselected++;
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}
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sprintf(buffer,"%d sequence in Clipboard",numselected);
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xv_set(frame,FRAME_RIGHT_FOOTER,buffer,0);
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xv_set(right_foot,PANEL_LABEL_STRING,buffer,0);
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return(XV_OK);
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}
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EditPaste(item,event)
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Panel_item item;
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Event *event;
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{
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extern Frame frame;
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extern Canvas EditCan,EditNameCan;
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extern NA_Alignment *DataSet,*Clipboard;
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extern Panel_item left_foot,right_foot;
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extern TextClipSize;
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int j,last = -1;
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if(TextClipSize != 0)
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{
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if(Clipboard->numelements == 0)
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return(EditSubPaste(item,event));
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else if(notice_prompt(frame,NULL,NOTICE_MESSAGE_STRINGS,
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"You have data in both clipboards, do you",
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"wish to paste from the...",
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NULL,
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NOTICE_BUTTON,"Sequence clipboard",1,
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NOTICE_BUTTON,"Text clipboard",2,
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0) == 2)
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return(EditSubPaste(item,event));
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}
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for(j=0;j<DataSet->numelements;j++)
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if(DataSet->element[j].selected)
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last = j;
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if(DataSet->maxnumelements <= DataSet->numelements+
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Clipboard->numelements)
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{
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DataSet->maxnumelements+=Clipboard->numelements;
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DataSet->element =(NA_Sequence*)Realloc(DataSet->element,
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DataSet->maxnumelements*sizeof(NA_Sequence));
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}
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for(j=DataSet->numelements-1;j>=last+1;j--)
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DataSet->element[j+Clipboard->numelements] =
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DataSet->element[j];
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for(j=0;j<Clipboard->numelements;j++)
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{
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DataSet->element[last+1+j] = Clipboard->element[j];
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/*
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* be sure to bring them back into alignment with the rest
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*/
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DataSet->element[last+1+j].offset -= DataSet->rel_offset;
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}
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DataSet->numelements += Clipboard->numelements;
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/*
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for(j=0;j<Clipboard->numelements;j++)
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{
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FreeNASeq(Clipboard->element[j]);
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InitNASeq(&(Clipboard->element[j]),TEXT);
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}
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*/
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Clipboard->numelements = 0;
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NormalizeOffset(DataSet);
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SetNADData(DataSet,EditCan,EditNameCan);
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Regroup(DataSet);
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RepaintAll(TRUE);
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xv_set(frame,FRAME_RIGHT_FOOTER,"Clipboard empty",0);
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xv_set(right_foot,PANEL_LABEL_STRING,"Clipboard empty",0);
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return(XV_OK);
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}
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Regroup(alignment)
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NA_Alignment *alignment;
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{
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int j,group,last;
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for(j=0;j<alignment->numelements;j++)
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{
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alignment->element[j].groupf = NULL;
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alignment->element[j].groupb = NULL;
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}
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for(group = 1;group <= alignment->numgroups;group++)
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{
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last = -1;
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for(j=0;j<alignment->numelements;j++)
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if(alignment->element[j].groupid == group)
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{
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if(last != -1)
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{
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alignment->element[j].groupb =
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&(alignment->element[last]);
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alignment->element[last].groupf =
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&(alignment->element[j]);
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}
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last = j;
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}
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}
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return;
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}
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EditSubCut(item,event)
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Panel_item item;
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Event *event;
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{
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extern Frame frame;
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extern Canvas EditCan,EditNameCan;
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extern NA_Alignment *DataSet,*Clipboard;
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extern Panel_item left_foot,right_foot;
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extern char **TextClip;
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extern int TextClipSize,TextClipLength;
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int blank_space = 0;
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NA_Sequence *this_elem;
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char buffer[80];
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int j,i,k,numselected=0,numshifted = 0,columns=0;
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/*
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* Check how many columns selected
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*/
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if(DataSet->selection_mask == NULL)
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return;
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for(j=0;j<DataSet->maxlen;j++)
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if(DataSet->selection_mask[j] == '1')
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columns++;
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if(columns == 0)
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return;
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/*
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* Free old Text clipboard
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*/
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if(SubCutViolate())
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{
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Warning("Cut violates current protections");
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return XV_OK;
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}
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for(j=0;j<TextClipSize;j++)
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Cfree(TextClip[j]);
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TextClipSize = 0;
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for(j=0;j<DataSet->numelements;j++)
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if(DataSet->element[j].subselected)
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TextClipSize++;
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if(TextClipSize == 0)
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return;
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TextClip = (char**)Calloc(TextClipSize,sizeof(char*));
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for(j=0;j<TextClipSize;j++)
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TextClip[j] = (char *)Calloc(columns,sizeof(char));
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for(j=0;j<DataSet->numelements;j++)
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if(DataSet->element[j].subselected)
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{
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this_elem = &(DataSet->element[j]);
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/*
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* Need to check protections
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*/
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for(i=0,blank_space = 0;i<this_elem->offset;i++)
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if(DataSet->selection_mask[i] == '1')
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TextClip[numselected][blank_space++] =
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(char)getelem(this_elem,i);
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for(i=0,k=0;i<this_elem->seqlen;i++)
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{
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if(DataSet->selection_mask[i+this_elem->offset]
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== '1')
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{
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if(this_elem->tmatrix)
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TextClip[numselected][k++] =
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this_elem->tmatrix[
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(char)getelem(this_elem,
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i+this_elem->offset)];
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else
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TextClip[numselected][k++] =
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(char)getelem(this_elem,
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i+this_elem->offset);
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}
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if((k!=0) && (i<this_elem->seqlen-1))
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{
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this_elem->sequence[1+i-k] =
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this_elem->sequence[1+i];
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if(this_elem->cmask)
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{
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this_elem->cmask[1+i-k] =
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this_elem->cmask[1+i];
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}
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}
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}
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numselected++;
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this_elem->seqlen -= k;
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this_elem->offset -= blank_space;
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/*
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* This might cause problems later on if the selection mask is
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* not cleaned...Make sure you test for subselected, not just
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* for a non-0 mask.
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*/
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this_elem->subselected = FALSE;
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}
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TextClipLength = columns;
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NormalizeOffset(DataSet);
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SetNADData(DataSet,EditCan,EditNameCan);
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Regroup(DataSet);
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RepaintAll(TRUE);
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sprintf(buffer,"%d bytes in Text Clipboard",numselected*columns);
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xv_set(frame,FRAME_RIGHT_FOOTER,buffer,0);
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xv_set(right_foot,PANEL_LABEL_STRING,buffer,0);
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return(XV_OK);
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}
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SubCutViolate()
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{
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int i,j;
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NA_Sequence *this_elem;
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extern NA_Alignment *DataSet;
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char base,tbase;
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int GAP=FALSE,UNAMB=FALSE,AMB=FALSE,prot;
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for(j=0;j<DataSet->numelements;j++)
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{
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this_elem = &(DataSet->element[j]);
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prot = this_elem->protect;
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if((this_elem->subselected)&& (this_elem->elementtype!=TEXT))
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{
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for(i=0;i<DataSet->maxlen;i++)
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if(DataSet->selection_mask[i] == '1')
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{
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base = (char)getelem(this_elem,i);
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if(this_elem->tmatrix)
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tbase = (this_elem->tmatrix[base])|32;
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switch(this_elem->elementtype)
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{
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case DNA:
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case RNA:
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if((base&15) == 0)
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GAP=TRUE;
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else if(tbase == 'n')
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AMB=TRUE;
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else
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UNAMB = TRUE;
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break;
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case PROTEIN:
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if(base == '-' ||
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base == '~' ||
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base == ' ')
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GAP=TRUE;
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else if(base == 'X' ||
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base == 'x')
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AMB=TRUE;
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else
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UNAMB = TRUE;
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break;
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case MASK:
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if(base == '0')
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GAP = TRUE;
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else
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UNAMB = TRUE;
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break;
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default:
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break;
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}
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if(((prot & PROT_WHITE_SPACE)==0) && GAP)
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return(TRUE);
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else if(((prot & PROT_GREY_SPACE)==0) && AMB)
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return(TRUE);
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else if(((prot & PROT_BASE_CHANGES)==0) &&
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UNAMB)
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return(TRUE);
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}
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}
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}
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return FALSE;
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}
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EditSubPaste(item,event)
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Panel_item item;
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Event *event;
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{
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extern Frame frame;
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extern Canvas EditCan,EditNameCan;
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extern NA_Alignment *DataSet,*Clipboard;
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extern Panel_item left_foot,right_foot;
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extern char **TextClip;
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extern int TextClipSize,TextClipLength;
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int *temp_cmask,cursorx,cursory;
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NA_Sequence *this_elem;
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char buffer[80];
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int j,i,k,violate = FALSE;
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if(DataSet->selection_mask == NULL)
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return(XV_OK);
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if(TextClipSize == 0 || TextClipLength==0)
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return(XV_OK);
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cursorx = ((NA_DisplayData*)(DataSet->na_ddata))->cursor_x;
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cursory = ((NA_DisplayData*)(DataSet->na_ddata))->cursor_y;
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if(cursory + TextClipSize > DataSet->numelements)
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{
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Warning("Can't paste a block there.");
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return(XV_OK);
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}
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for(j=0;j<TextClipSize;j++)
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{
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this_elem = &(DataSet->element[j+cursory]);
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violate |= InsertViolate(DataSet,this_elem,
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TextClip[j],cursorx,TextClipLength);
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}
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if(violate == FALSE)
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{
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for(j=0;j<TextClipSize;j++)
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{
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this_elem = &(DataSet->element[j+cursory]);
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InsertNA(this_elem,TextClip[j],TextClipLength,cursorx);
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}
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}
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RepaintAll(TRUE);
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sprintf(buffer,"%d bytes in Text Clipboard",TextClipLength *
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TextClipSize);
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xv_set(frame,FRAME_RIGHT_FOOTER,buffer,0);
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xv_set(right_foot,PANEL_LABEL_STRING,buffer,0);
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return(XV_OK);
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}
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EditSubCopy(item,event)
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Panel_item item;
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Event *event;
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{
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extern Frame frame;
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extern Canvas EditCan,EditNameCan;
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extern NA_Alignment *DataSet,*Clipboard;
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extern Panel_item left_foot,right_foot;
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extern char **TextClip;
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extern int TextClipSize,TextClipLength;
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int blank_space = 0;
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NA_Sequence *this_elem;
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char buffer[80];
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int j,i,k,numselected=0,numshifted = 0,columns=0;
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/*
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* Check how many columns selected
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*/
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if(DataSet->selection_mask == NULL)
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return;
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for(j=0;j<DataSet->maxlen;j++)
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if(DataSet->selection_mask[j] == '1')
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columns++;
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if(columns == 0)
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return;
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/*
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* Free old Text clipboard
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*/
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for(j=0;j<TextClipSize;j++)
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Cfree(TextClip[j]);
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TextClipSize = 0;
|
|
|
|
for(j=0;j<DataSet->numelements;j++)
|
|
if(DataSet->element[j].subselected)
|
|
TextClipSize++;
|
|
|
|
if(TextClipSize == 0)
|
|
return;
|
|
|
|
TextClip = (char**)Calloc(TextClipSize,sizeof(char*));
|
|
|
|
for(j=0;j<TextClipSize;j++)
|
|
TextClip[j] = (char *)Calloc(columns,sizeof(char));
|
|
|
|
|
|
for(j=0;j<DataSet->numelements;j++)
|
|
if(DataSet->element[j].subselected)
|
|
{
|
|
this_elem = &(DataSet->element[j]);
|
|
/*
|
|
* Need to check protections
|
|
*/
|
|
|
|
for(i=0,blank_space = 0;i<this_elem->offset;i++)
|
|
if(DataSet->selection_mask[i] == '1')
|
|
TextClip[numselected][blank_space++] =
|
|
(char)getelem(this_elem,i);
|
|
|
|
|
|
for(i=0,k=0;i<this_elem->seqlen;i++)
|
|
{
|
|
if(DataSet->selection_mask[i+this_elem->offset]
|
|
== '1')
|
|
{
|
|
if(this_elem->tmatrix)
|
|
TextClip[numselected][k++] =
|
|
this_elem->tmatrix[
|
|
(char)getelem(this_elem,
|
|
i+this_elem->offset)];
|
|
else
|
|
TextClip[numselected][k++] =
|
|
(char)getelem(this_elem,
|
|
i+this_elem->offset);
|
|
}
|
|
|
|
}
|
|
|
|
numselected++;
|
|
this_elem->subselected = FALSE;
|
|
}
|
|
|
|
TextClipLength = columns;
|
|
|
|
SetNADData(DataSet,EditCan,EditNameCan);
|
|
|
|
RepaintAll(TRUE);
|
|
|
|
sprintf(buffer,"%d bytes in Text Clipboard",numselected*columns);
|
|
xv_set(frame,FRAME_RIGHT_FOOTER,buffer,0);
|
|
xv_set(right_foot,PANEL_LABEL_STRING,buffer,0);
|
|
|
|
return(XV_OK);
|
|
}
|
|
|
|
int TestSelection()
|
|
{
|
|
int j,select_mode = 0,selected = 0,subselected = 0;
|
|
extern NA_Alignment *DataSet;
|
|
extern Frame frame;
|
|
|
|
for(j=0;j<((NA_Alignment*)DataSet)->numelements;j++)
|
|
{
|
|
selected|=((NA_Alignment*)DataSet)->element[j].selected;
|
|
subselected|=((NA_Alignment*)DataSet)->element[j].subselected;
|
|
}
|
|
|
|
if (!(selected || subselected))
|
|
Warning("Warning, no sequences selected");
|
|
|
|
if(selected && !subselected)
|
|
select_mode = SELECTED;
|
|
|
|
if(!selected && subselected)
|
|
select_mode = SELECT_REGION;
|
|
|
|
if(selected && subselected)
|
|
select_mode = notice_prompt(frame,NULL,NOTICE_MESSAGE_STRINGS,
|
|
"Do you want to use the...",NULL,
|
|
NOTICE_BUTTON,"Selected sequences",SELECTED,
|
|
NOTICE_BUTTON,"Selected regions",SELECT_REGION,
|
|
NULL);
|
|
/*
|
|
for(j=0;j<((NA_Alignment*)DataSet)->numelements;j++)
|
|
{
|
|
if(select_mode == SELECT_REGION)
|
|
((NA_Alignment*)DataSet)->element[j].selected = FALSE;
|
|
else
|
|
((NA_Alignment*)DataSet)->element[j].subselected = FALSE;
|
|
}
|
|
*/
|
|
|
|
return(select_mode);
|
|
}
|
|
|