/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
\r
int findSeq(MouseEvent evt)\r
{\r
-\r
int seq = 0;\r
int y = evt.getY();\r
\r
\r
y -= hgap;\r
\r
- seq = ( (y % cHeight) / av.getCharHeight());\r
+ seq = Math.min( (y % cHeight) / av.getCharHeight(),\r
+ av.alignment.getHeight() -1);\r
}\r
else\r
{\r
- seq = (y / av.getCharHeight()) + av.getStartSeq();\r
+ seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),\r
+ av.alignment.getHeight() -1);\r
}\r
\r
return seq;\r
SequenceGroup sg = av.selectionGroup;\r
//Find the top and bottom of this group\r
int min = av.alignment.getHeight(), max = 0;\r
- for(int i=0; i<sg.getSize(); i++)\r
+ for(int i=0; i<sg.getSize(false); i++)\r
{\r
int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
if(index > max)\r
else\r
{\r
// Now add any sequences between min and max\r
- sg.sequences.clear();\r
+ sg.getSequences(false).clear();\r
for (int i = min; i < max; i++)\r
{\r
sg.addSequence(av.alignment.getSequenceAt(i), false);\r
\r
editOccurred();\r
\r
- endEditing();\r
ap.repaint();\r
}\r
\r
boolean fixedColumns = false;\r
SequenceGroup sg = av.getSelectionGroup();\r
\r
- if(groupEditing && sg==null)\r
- return;\r
\r
if (!groupEditing && av.hasHiddenRows)\r
{\r
- //This needs to check all the sequences in a group edit,m\r
- // not just the startseq\r
if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
{\r
groupEditing = true;\r
}\r
}\r
\r
+ //No group, but the sequence may represent a group\r
+ if (groupEditing\r
+ && sg == null\r
+ && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)\r
+ {\r
+ groupEditing = false;\r
+ }\r
+\r
SequenceI seq = av.alignment.getSequenceAt(startseq);\r
StringBuffer message = new StringBuffer();\r
if (groupEditing)\r
message.append("Edit group:");\r
else\r
- message.append("Edit sequence: "+seq.getName());\r
+ message.append("Edit sequence: "+seq.getName());\r
\r
if(insertGap)\r
message.append(" insert ");\r
\r
//Are we editing within a selection group?\r
if (groupEditing\r
- || (sg != null && sg.sequences.contains(seq)))\r
+ || (sg != null && sg.getSequences(true).contains(seq)))\r
{\r
fixedColumns = true;\r
\r
+ //sg might be null as the user may only see 1 sequence,\r
+ //but the sequence represents a group\r
+ if (sg == null)\r
+ {\r
+ sg = new SequenceGroup(null, null, false, false, false, 0,\r
+ av.alignment.getWidth()-1);\r
+ sg.addSequence(av.alignment.getSequenceAt(startseq), false);\r
+ }\r
+\r
fixedLeft = sg.getStartRes();\r
fixedRight = sg.getEndRes();\r
\r
}\r
\r
\r
-\r
- if(av.hasHiddenColumns)\r
+ if(av.hasHiddenColumns )\r
{\r
- fixedColumns = true;\r
- int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);\r
- int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);\r
-\r
- if( ( insertGap && startres>y1 && lastres<y1)\r
- || (!insertGap && startres<y2 && lastres>y2) )\r
- {\r
- endEditing();\r
- return;\r
- }\r
+ fixedColumns = true;\r
+ int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);\r
+ int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);\r
\r
- if(fixedRight<y2 && fixedRight==-1 && y2!=startres)\r
- fixedRight = y2 -1;\r
- if(y1>fixedLeft && fixedLeft==-1)\r
- fixedLeft = y1;\r
- }\r
-\r
- if (groupEditing)\r
- {\r
-\r
- /*if (av.hasHiddenRows)\r
- {\r
- //sg might be null as the user may only see 1 sequence\r
- if (sg == null)\r
+ if ( (insertGap && startres > y1 && lastres < y1)\r
+ || (!insertGap && startres < y2 && lastres > y2))\r
{\r
- sg = new SequenceGroup();\r
- sg.addSequence(av.alignment.getSequenceAt(startseq), false);\r
+ endEditing();\r
+ return;\r
}\r
\r
- SequenceGroup tmp = new SequenceGroup();\r
-\r
- //Do any of the sequences have hidden associates?\r
- for (int s = 0; s < sg.getSize(); s++)\r
+ //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");\r
+ //Selection spans a hidden region\r
+ if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))\r
{\r
- seq = sg.getSequenceAt(s);\r
- tmp.addSequence(seq, false);\r
- if (seq.getHiddenSequences() != null)\r
+ if(startres>=y2)\r
{\r
- for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)\r
- tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),\r
- false);\r
+ fixedLeft = y2;\r
}\r
+ else\r
+ {\r
+ fixedRight = y2 - 1;\r
+ }\r
}\r
-\r
- sg = tmp;\r
- }*/\r
- // int blankColumn = -1;\r
+ }\r
\r
\r
+ if (groupEditing)\r
+ {\r
// drag to right\r
if (insertGap)\r
{\r
//If the user has selected the whole sequence, and is dragging to\r
// the right, we can still extend the alignment and selectionGroup\r
- if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth())\r
+ if( sg.getStartRes() == 0\r
+ && sg.getEndRes() == fixedRight\r
+ && sg.getEndRes() == av.alignment.getWidth()-1\r
+ )\r
{\r
sg.setEndRes(av.alignment.getWidth() + startres - lastres);\r
fixedRight = sg.getEndRes();\r
fixedRight--)\r
{\r
blank = true;\r
- for (int s = 0; s < sg.getSize(); s++)\r
+ for (int s = 0; s < sg.getSize(true); s++)\r
{\r
- seq = sg.getSequenceAt(s);\r
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
for (int j = 0; j < startres - lastres; j++)\r
{\r
if (!jalview.util.Comparison.isGap(\r
\r
if (!blank)\r
{\r
- if(sg.getSize() == av.alignment.getHeight())\r
+ if(sg.getSize(false) == av.alignment.getHeight() )\r
{\r
+ if((av.hasHiddenColumns\r
+ && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ int alWidth = av.alignment.getWidth();\r
+ if(av.hasHiddenRows)\r
+ {\r
+ int hwidth = av.alignment.getHiddenSequences().getWidth();\r
+ if(hwidth>alWidth)\r
+ alWidth = hwidth;\r
+ }\r
//We can still insert gaps if the selectionGroup\r
//contains all the sequences\r
sg.setEndRes(sg.getEndRes()+startres-lastres);\r
- fixedRight = av.alignment.getWidth()+startres-lastres;\r
+ fixedRight = alWidth+startres-lastres;\r
}\r
else\r
{\r
/// Are we able to delete?\r
// ie are all columns blank?\r
\r
- for (int s = 0; s < sg.getSize(); s++)\r
+ for (int s = 0; s < sg.getSize(true); s++)\r
{\r
- seq = sg.getSequenceAt(s);\r
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
\r
for (int j = startres; j < lastres; j++)\r
{\r
}\r
\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ for (int i = 0; i < sg.getSize(true); i++)\r
{\r
- seq = sg.getSequenceAt(i);\r
+ seq = (SequenceI) sg.getSequences(true).elementAt(i);\r
\r
if (insertGap)\r
{\r
{\r
if (fixedColumns && fixedRight != -1)\r
{\r
- if (sg.getStartRes() == 0\r
- && sg.getEndRes() + 1 == av.alignment.getWidth()\r
- && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))\r
- {\r
- //Single sequence edit, whole sequence selected,\r
- //extend the selection group\r
- sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);\r
- fixedColumns = false;\r
- insertChar(j, seq);\r
- }\r
- else\r
insertChar(j, seq, fixedRight);\r
}\r
else\r
\r
if (blankColumn <= j)\r
{\r
+ blankColumn = fixedColumn;\r
endEditing();\r
return;\r
}\r
stretchGroup = null;\r
}\r
}\r
- else if (!stretchGroup.sequences.contains(sequence) ||\r
+ else if (!stretchGroup.getSequences(false).contains(sequence) ||\r
(stretchGroup.getStartRes() > res) ||\r
(stretchGroup.getEndRes() < res))\r
{\r
\r
}\r
\r
- if (av.cursorMode)\r
- {\r
- seqCanvas.cursorX = findRes(evt);\r
- seqCanvas.cursorY = findSeq(evt);\r
- seqCanvas.repaint();\r
- return;\r
- }\r
-\r
\r
if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
{\r
Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),\r
sequence.findPosition(res));\r
- Vector links = new Vector();;\r
+ Vector links = new Vector();\r
for (int i = 0; i < allFeatures.size(); i++)\r
{\r
SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);\r
}\r
}\r
\r
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+ return;\r
+ }\r
\r
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);\r
- pop.show(this, evt.getX(), evt.getY());\r
+ if (av.cursorMode)\r
+ {\r
+ seqCanvas.cursorX = findRes(evt);\r
+ seqCanvas.cursorY = findSeq(evt);\r
+ seqCanvas.repaint();\r
+ return;\r
}\r
- else if (stretchGroup == null)\r
+\r
+ if (stretchGroup == null)\r
{\r
//Only if left mouse button do we want to change group sizes\r
\r
{\r
if (stretchGroup.cs instanceof ClustalxColourScheme)\r
{\r
- ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
- sequences,\r
+ ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
+ stretchGroup.getSequences(true),\r
stretchGroup.getWidth());\r
}\r
\r
return;\r
}\r
\r
-\r
- if(y > av.alignment.getHeight())\r
- {\r
- y = av.alignment.getHeight() -1;\r
- }\r
if(res> av.alignment.getWidth())\r
{\r
res = av.alignment.getWidth()-1;\r
\r
Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
\r
- if (stretchGroup.sequences.contains(nextSeq))\r
+ if (stretchGroup.getSequences(false).contains(nextSeq))\r
{\r
stretchGroup.deleteSequence(seq, false);\r
}\r
git://source.jalview.org / jalview.git / blobdiff