/*\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
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.removeAllElements();\r
+ sg.getSequences(false).removeAllElements();\r
for (int i = min; i < max; i++)\r
{\r
sg.addSequence(av.alignment.getSequenceAt(i), false);\r
res = (x / av.getCharWidth()) + av.getStartRes();\r
}\r
\r
+ if(av.hasHiddenColumns)\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+\r
return res;\r
\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
+ if(seq<0)\r
+ seq = 0;\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
+ if(seq<0)\r
+ seq = 0;\r
}\r
\r
return seq;\r
\r
if (obj != null)\r
{\r
-\r
if (obj != "")\r
{\r
- text.append(obj + " (" +\r
- av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
+ text.append(obj + " (" + sequence.findPosition(res) + ")");\r
}\r
}\r
\r
seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
}\r
\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
\r
// use aa to see if the mouse pointer is on a\r
if (av.showSequenceFeatures\r
\r
tooltip.repaint();\r
\r
- // text.append(" Sequence Feature:");\r
- // text.append(featureText);\r
-\r
}\r
-\r
-\r
- ap.alignFrame.statusBar.setText(text.toString());\r
-\r
}\r
\r
Vector getAllFeaturesAtRes(SequenceI seq, int res)\r
}\r
\r
synchronized void editSequence(boolean insertGap, int startres)\r
- {\r
- int fixedLeft = -1;\r
- int fixedRight = -1;\r
- boolean fixedColumns = false;\r
- SequenceGroup sg = av.getSelectionGroup();\r
+ {\r
+ int fixedLeft = -1;\r
+ int fixedRight = -1;\r
+ boolean fixedColumns = false;\r
+ SequenceGroup sg = av.getSelectionGroup();\r
\r
- if(groupEditing && sg==null)\r
- return;\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
+ if (!groupEditing && av.hasHiddenRows)\r
+ {\r
+ if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
+ {\r
+ groupEditing = true;\r
+ }\r
+ }\r
\r
- if(insertGap)\r
- message.append(" insert ");\r
- else\r
- message.append(" delete ");\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
+\r
+ if(insertGap)\r
+ message.append(" insert ");\r
+ else\r
+ message.append(" delete ");\r
+\r
+ message.append(Math.abs(startres-lastres)+" gaps.");\r
+ ap.alignFrame.statusBar.setText(message.toString());\r
\r
- message.append(Math.abs(startres-lastres)+" gaps.");\r
- ap.alignFrame.statusBar.setText(message.toString());\r
\r
+ //Are we editing within a selection group?\r
+ if (groupEditing\r
+ || (sg != null && sg.getSequences(true).contains(seq)))\r
+ {\r
+ fixedColumns = true;\r
\r
- //Are we editing within a selection group?\r
- if (groupEditing\r
- || (sg != null && sg.sequences.contains(seq)))\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
- fixedColumns = true;\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
+ fixedLeft = sg.getStartRes();\r
+ fixedRight = sg.getEndRes();\r
\r
- if ( (startres < fixedLeft && lastres >= fixedLeft)\r
- || (startres >= fixedLeft && lastres < fixedLeft)\r
- || (startres > fixedRight && lastres <=fixedRight)\r
- || (startres <= fixedRight && lastres > fixedRight))\r
+ if ( (startres < fixedLeft && lastres >= fixedLeft)\r
+ || (startres >= fixedLeft && lastres < fixedLeft)\r
+ || (startres > fixedRight && lastres <=fixedRight)\r
+ || (startres <= fixedRight && lastres > fixedRight))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ if (fixedLeft > startres)\r
+ {\r
+ fixedRight = fixedLeft - 1;\r
+ fixedLeft = 0;\r
+ }\r
+ else if (fixedRight < startres)\r
+ {\r
+ fixedLeft = fixedRight;\r
+ fixedRight = -1;\r
+ }\r
+ }\r
+\r
+\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
\r
- if (fixedLeft > startres)\r
- {\r
- fixedRight = fixedLeft - 1;\r
- fixedLeft = 0;\r
- }\r
- else if (fixedRight < startres)\r
+ //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");\r
+ //Selection spans a hidden region\r
+ if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))\r
{\r
- fixedLeft = fixedRight;\r
- fixedRight = -1;\r
+ if(startres>=y2)\r
+ {\r
+ fixedLeft = y2;\r
+ }\r
+ else\r
+ {\r
+ fixedRight = y2 - 1;\r
+ }\r
}\r
- }\r
+ }\r
\r
\r
- if (groupEditing)\r
+ if (groupEditing)\r
+ {\r
+ // drag to right\r
+ if (insertGap)\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
- {\r
- sg.setEndRes(av.alignment.getWidth() + startres - lastres);\r
- fixedRight = sg.getEndRes();\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\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
+ }\r
\r
- // Is it valid with fixed columns??\r
- // Find the next gap before the end\r
- // of the visible region boundary\r
- boolean blank = false;\r
- for (fixedRight = fixedRight;\r
- fixedRight > lastres;\r
- fixedRight--)\r
+ // Is it valid with fixed columns??\r
+ // Find the next gap before the end\r
+ // of the visible region boundary\r
+ boolean blank = false;\r
+ for (fixedRight = fixedRight;\r
+ fixedRight > lastres;\r
+ fixedRight--)\r
+ {\r
+ blank = true;\r
+ for (int s = 0; s < sg.getSize(true); s++)\r
{\r
- blank = true;\r
- for (int s = 0; s < sg.getSize(); s++)\r
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
+ for (int j = 0; j < startres - lastres; j++)\r
{\r
- seq = sg.getSequenceAt(s);\r
- for (int j = 0; j < startres - lastres; j++)\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getCharAt(fixedRight - j)))\r
{\r
- if (!jalview.util.Comparison.isGap(\r
- seq.getCharAt(fixedRight - j)))\r
- {\r
- blank = false;\r
- break;\r
- }\r
+ blank = false;\r
+ break;\r
}\r
}\r
- if (blank)\r
- break;\r
}\r
+ if (blank)\r
+ break;\r
+ }\r
\r
- if (!blank)\r
+ if (!blank)\r
+ {\r
+ if(sg.getSize(false) == av.alignment.getHeight() )\r
{\r
- if(sg.getSize() == av.alignment.getHeight())\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
- }\r
- else\r
+ if((av.hasHiddenColumns\r
+ && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
{\r
endEditing();\r
return;\r
}\r
- }\r
- }\r
-\r
\r
- // drag to left\r
- else if(!insertGap)\r
- {\r
- /// Are we able to delete?\r
- // ie are all columns blank?\r
-\r
- for (int s = 0; s < sg.getSize(); s++)\r
- {\r
- seq = sg.getSequenceAt(s);\r
-\r
- for (int j = startres; j < lastres; j++)\r
+ int alWidth = av.alignment.getWidth();\r
+ if(av.hasHiddenRows)\r
{\r
- if (seq.getSequence().length() <= j)\r
- {\r
- continue;\r
- }\r
-\r
- if (!jalview.util.Comparison.isGap(\r
- seq.getSequence().charAt(j)))\r
- {\r
- // Not a gap, block edit not valid\r
- endEditing();\r
- return;\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 = alWidth+startres-lastres;\r
+ }\r
+ else\r
+ {\r
+ endEditing();\r
+ return;\r
}\r
}\r
+ }\r
+\r
\r
+ // drag to left\r
+ else if(!insertGap)\r
+ {\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ for (int s = 0; s < sg.getSize(true); s++)\r
{\r
- seq = sg.getSequenceAt(i);\r
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
\r
- if (insertGap)\r
+ for (int j = startres; j < lastres; j++)\r
{\r
- // dragging to the right\r
- for (int j = lastres; j < startres; j++)\r
+ if (seq.getSequence().length() <= j)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- insertChar(j, seq, fixedRight);\r
- }\r
- else\r
- insertChar(j, seq);\r
+ continue;\r
}\r
- }\r
- else\r
- {\r
- // dragging to the left\r
- for (int j = lastres; j > startres; j--)\r
+\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getSequence().charAt(j)))\r
{\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- deleteChar(startres, seq, fixedRight);\r
- }\r
- else\r
- {\r
- deleteChar(startres, seq);\r
- }\r
+ // Not a gap, block edit not valid\r
+ endEditing();\r
+ return;\r
}\r
}\r
}\r
}\r
- else /////Editing a single sequence///////////\r
+\r
+\r
+ for (int i = 0; i < sg.getSize(true); i++)\r
{\r
+ seq = (SequenceI) sg.getSequences(true).elementAt(i);\r
+\r
if (insertGap)\r
{\r
// dragging to the right\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
+ insertChar(j, seq, fixedRight);\r
}\r
else\r
insertChar(j, seq);\r
}\r
}\r
}\r
+ }\r
+ else /////Editing a single sequence///////////\r
+ {\r
+ if (insertGap)\r
+ {\r
+ // dragging to the right\r
+ for (int j = lastres; j < startres; j++)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ insertChar(j, seq, fixedRight);\r
+ }\r
+ else\r
+ insertChar(j, seq);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ deleteChar(startres, seq, fixedRight);\r
+ }\r
+ else\r
+ {\r
+ deleteChar(startres, seq);\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- lastres = startres;\r
- seqCanvas.repaint();\r
- }\r
+ lastres = startres;\r
+ seqCanvas.repaint();\r
+ }\r
\r
\r
/**\r
}\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
av.setSelectionGroup(stretchGroup);\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
\r
// DETECT RIGHT MOUSE BUTTON IN AWT\r
if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
this.add(popup);\r
popup.show(this, evt.getX(), evt.getY());\r
ap.repaint();\r
+ return;\r
}\r
- else\r
+\r
+ if (av.cursorMode)\r
{\r
+ seqCanvas.cursorX = findRes(evt);\r
+ seqCanvas.cursorY = findSeq(evt);\r
+ seqCanvas.repaint();\r
+ return;\r
+ }\r
+\r
//Only if left mouse button do we want to change group sizes\r
\r
if (stretchGroup == null)\r
}\r
\r
}\r
-\r
- if (stretchGroup != null && stretchGroup.getEndRes() == res)\r
- {\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
- }\r
-\r
- else if (stretchGroup != null && stretchGroup.getStartRes() == res)\r
- {\r
- // Edit end res position of selected group\r
- changeStartRes = true;\r
- }\r
- }\r
}\r
\r
public void doMouseReleasedDefineMode(MouseEvent evt)\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
\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
}\r
}\r
\r
+ void scrollCanvas(MouseEvent evt)\r
+ {\r
+ if(evt==null)\r
+ {\r
+ if(scrollThread!=null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+ mouseDragging = false;\r
+ }\r
+ else\r
+ {\r
+ if (scrollThread == null)\r
+ scrollThread = new ScrollThread();\r
+\r
+ mouseDragging = true;\r
+ scrollThread.setEvent(evt);\r
+ }\r
+\r
+ }\r
+\r
// this class allows scrolling off the bottom of the visible alignment\r
class ScrollThread\r
extends Thread\r
\r
if (mouseDragging && evt.getX() < 0)\r
{\r
- running = ap.scrollRight(true);\r
+ running = ap.scrollRight(false);\r
}\r
\r
else if (mouseDragging && evt.getX() >= getSize().width)\r
{\r
- running = ap.scrollRight(false);\r
+ running = ap.scrollRight(true);\r
}\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff