/*\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
import javax.swing.*;\r
\r
+import java.util.Vector;\r
+\r
\r
/**\r
* DOCUMENT ME!\r
public AlignmentPanel ap;\r
protected int lastres;\r
protected int startseq;\r
- int startEdit = -1;\r
- int endEdit = -1;\r
protected AlignViewport av;\r
\r
// if character is inserted or deleted, we will need to recalculate the conservation\r
SequenceGroup stretchGroup = null;\r
boolean remove = false;\r
\r
+ Point lastMousePress;\r
boolean mouseWheelPressed = false;\r
+ StringBuffer keyboardNo1;\r
+ StringBuffer keyboardNo2;\r
+\r
+ java.net.URL linkImageURL;\r
\r
/**\r
* Creates a new SeqPanel object.\r
*/\r
public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
{\r
+ linkImageURL = getClass().getResource("/images/link.gif");\r
ToolTipManager.sharedInstance().registerComponent(this);\r
ToolTipManager.sharedInstance().setInitialDelay(0);\r
ToolTipManager.sharedInstance().setDismissDelay(10000);\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
}\r
\r
+ Vector getAllFeaturesAtRes(SequenceI seq, int res)\r
+ {\r
+ Vector allFeatures = new Vector();\r
+ int index = 0;\r
+ if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null)\r
+ {\r
+ while (index < seq.getSequenceFeatures().length)\r
+ {\r
+ SequenceFeature sf = seq.getSequenceFeatures()[index];\r
+ if (sf.getBegin() <= res &&\r
+ sf.getEnd() >= res)\r
+ {\r
+ if (av.featuresDisplayed.containsKey(sf.getType()))\r
+ {\r
+ allFeatures.addElement(sf);\r
+ }\r
+ }\r
+ index++;\r
+ }\r
+ }\r
+ return allFeatures;\r
+ }\r
+\r
void endEditing()\r
{\r
startseq = -1;\r
seqEditOccurred = false;\r
editingSeqs = false;\r
groupEditing = false;\r
+ keyboardNo1 = null;\r
+ keyboardNo2 = null;\r
+ }\r
+\r
+ void setCursorRow()\r
+ {\r
+ seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;\r
+ scrollToVisible();\r
}\r
\r
+ void setCursorColumn()\r
+ {\r
+ seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;\r
+ scrollToVisible();\r
+ }\r
+\r
+ void setCursorRowAndColumn()\r
+ {\r
+ if(keyboardNo2==null)\r
+ {\r
+ keyboardNo2 = new StringBuffer();\r
+ }\r
+ else\r
+ {\r
+ seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;\r
+ seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;\r
+ scrollToVisible();\r
+ }\r
+ }\r
+\r
+ void setCursorPosition()\r
+ {\r
+ SequenceI sequence =\r
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
+\r
+ seqCanvas.cursorX = sequence.findIndex(\r
+ getKeyboardNo(keyboardNo1)-1\r
+ );\r
+ scrollToVisible();\r
+ }\r
+\r
+ void moveCursor(int dx, int dy)\r
+ {\r
+ seqCanvas.cursorX += dx;\r
+ seqCanvas.cursorY += dy;\r
+ scrollToVisible();\r
+ }\r
+\r
+ void scrollToVisible()\r
+ {\r
+ if (seqCanvas.cursorX < 0)\r
+ seqCanvas.cursorX = 0;\r
+ else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)\r
+ seqCanvas.cursorX = av.alignment.getWidth() - 1;\r
+\r
+ if (seqCanvas.cursorY < 0)\r
+ seqCanvas.cursorY = 0;\r
+ else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)\r
+ seqCanvas.cursorY = av.alignment.getHeight() - 1;\r
+\r
+\r
+ endEditing();\r
+ if(av.wrapAlignment)\r
+ {\r
+ ap.scrollToWrappedVisible(seqCanvas.cursorX);\r
+ }\r
+ else\r
+ {\r
+ while (seqCanvas.cursorY < av.startSeq)\r
+ {\r
+ ap.scrollUp(true);\r
+ }\r
+ while (seqCanvas.cursorY + 1 > av.endSeq)\r
+ {\r
+ ap.scrollUp(false);\r
+ }\r
+ if (!av.wrapAlignment)\r
+ {\r
+ while (seqCanvas.cursorX < av.startRes)\r
+ {\r
+ if (!ap.scrollRight(false))\r
+ break;\r
+ }\r
+ while (seqCanvas.cursorX > av.endRes)\r
+ {\r
+ if (!ap.scrollRight(true))\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),\r
+ seqCanvas.cursorX, seqCanvas.cursorY);\r
+\r
+ seqCanvas.repaint();\r
+ }\r
+\r
+ void setSelectionAreaAtCursor(boolean topLeft)\r
+ {\r
+ SequenceI sequence =\r
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
+\r
+ if(av.getSelectionGroup()!=null)\r
+ {\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(false); i++)\r
+ {\r
+ int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
+ if(index > max)\r
+ max = index;\r
+ if(index < min)\r
+ min = index;\r
+ }\r
+\r
+ max ++;\r
+\r
+ if(topLeft)\r
+ {\r
+ sg.setStartRes(seqCanvas.cursorX);\r
+ if(sg.getEndRes()<seqCanvas.cursorX)\r
+ sg.setEndRes(seqCanvas.cursorX);\r
+\r
+ min = seqCanvas.cursorY;\r
+ }\r
+ else\r
+ {\r
+ sg.setEndRes(seqCanvas.cursorX);\r
+ if(sg.getStartRes()>seqCanvas.cursorX)\r
+ sg.setStartRes(seqCanvas.cursorX);\r
+\r
+ max = seqCanvas.cursorY+1;\r
+ }\r
+\r
+ if(min>max)\r
+ {\r
+ // Only the user can do this\r
+ av.setSelectionGroup(null);\r
+ }\r
+ else\r
+ {\r
+ // Now add any sequences between min and max\r
+ sg.getSequences(false).clear();\r
+ for (int i = min; i < max; i++)\r
+ {\r
+ sg.addSequence(av.alignment.getSequenceAt(i), false);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (av.getSelectionGroup() == null)\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setStartRes(seqCanvas.cursorX);\r
+ sg.setEndRes(seqCanvas.cursorX);\r
+ sg.addSequence(sequence, false);\r
+ av.setSelectionGroup(sg);\r
+ }\r
+\r
+\r
+ ap.repaint();\r
+ }\r
+\r
+ void insertGapAtCursor(boolean group)\r
+ {\r
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
+ av.alignment, HistoryItem.EDIT));\r
+ groupEditing = group;\r
+ startseq = seqCanvas.cursorY;\r
+ lastres = seqCanvas.cursorX;\r
+ editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));\r
+ editOccurred();\r
+ }\r
+\r
+ void deleteGapAtCursor(boolean group)\r
+ {\r
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
+ av.alignment, HistoryItem.EDIT));\r
+ groupEditing = group;\r
+ startseq = seqCanvas.cursorY;\r
+ lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);\r
+ editSequence(false, seqCanvas.cursorX);\r
+ editOccurred();\r
+ }\r
+\r
+ void numberPressed(char value)\r
+ {\r
+ if(keyboardNo1==null)\r
+ keyboardNo1 = new StringBuffer();\r
+\r
+ if(keyboardNo2!=null)\r
+ keyboardNo2.append(value);\r
+ else\r
+ keyboardNo1.append(value);\r
+ }\r
+\r
+ int getKeyboardNo(StringBuffer kb)\r
+ {\r
+ if(kb==null)\r
+ return 1;\r
+ else\r
+ return Integer.parseInt(kb.toString());\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
public void mouseReleased(MouseEvent evt)\r
{\r
mouseDragging = false;\r
+ mouseWheelPressed = false;\r
\r
if (!editingSeqs)\r
{\r
return;\r
}\r
\r
- if (seqEditOccurred)\r
- {\r
- editOccurred();\r
- }\r
+ editOccurred();\r
\r
- endEditing();\r
- ap.repaint();\r
+ ap.repaint();\r
}\r
\r
\r
*/\r
public void mousePressed(MouseEvent evt)\r
{\r
+ lastMousePress = evt.getPoint();\r
+\r
if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
{\r
mouseWheelPressed = true;\r
}\r
\r
\r
- ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
- av.alignment, HistoryItem.EDIT));\r
\r
int seq = findSeq(evt);\r
int res = findRes(evt);\r
if(seq<0 || res<0)\r
return;\r
\r
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
+ av.alignment, HistoryItem.EDIT));\r
+\r
if ((seq < av.getAlignment().getHeight()) &&\r
(res < av.getAlignment().getSequenceAt(seq).getLength()))\r
{\r
lastres = -1;\r
}\r
\r
- startEdit = lastres;\r
- endEdit = lastres;\r
-\r
return;\r
}\r
\r
int res = findRes(evt);\r
int seq = findSeq(evt);\r
\r
+\r
if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())\r
return;\r
\r
seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
}\r
\r
-\r
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
- sequence.getName());\r
-\r
- Object obj = null;\r
- if (av.alignment.isNucleotide())\r
- {\r
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
- "");\r
- if(obj!=null)\r
- text.append(" Nucleotide: ");\r
- }\r
- else\r
- {\r
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
- if(obj!=null)\r
- text.append(" Residue: ");\r
- }\r
-\r
- if (obj != null)\r
- {\r
-\r
- if (obj != "")\r
- {\r
- text.append( obj + " (" +\r
- av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
- }\r
- }\r
-\r
- ap.alignFrame.statusBar.setText(text.toString());\r
+ setStatusMessage(sequence, res, seq);\r
\r
// use aa to see if the mouse pointer is on a\r
if (av.showSequenceFeatures)\r
if(features!=null)\r
{\r
StringBuffer sbuffer = new StringBuffer("<html>");\r
+ StringBuffer seqSpecific = new StringBuffer();\r
\r
for (int i = 0; i < features.length; i++)\r
{\r
if ( (features[i].getBegin() <= sequence.findPosition(res)) &&\r
(features[i].getEnd() >= sequence.findPosition(res)))\r
{\r
- if(!av.featuresDisplayed.containsKey(features[i].getType()))\r
+ if(av.featuresDisplayed==null\r
+ || !av.featuresDisplayed.containsKey(features[i].getType()))\r
continue;\r
\r
\r
sbuffer.append("<br>");\r
sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +\r
features[i].getEnd());\r
+ if (features[i].links != null)\r
+ sbuffer.append(" <img src=\"" + linkImageURL + "\">");\r
}\r
}\r
else\r
{\r
if (sbuffer.length() > 6)\r
sbuffer.append("<br>");\r
- if(features[i].featureGroup!=null)\r
- sbuffer.append(features[i].featureGroup+";");\r
\r
- sbuffer.append(features[i].getType());\r
+ sbuffer.append(features[i].getType() + " " +\r
+ features[i].begin);\r
+ if (features[i].begin != features[i].end)\r
+ sbuffer.append(" " + features[i].end);\r
\r
if (features[i].getDescription() != null\r
&& !features[i].description.equals(features[i].getType()))\r
sbuffer.append("; " + features[i].getDescription());\r
\r
- if (features[i].getStatus() != null && features[i].getStatus().length()>0)\r
+ if (features[i].getValue("status") != null)\r
{\r
- sbuffer.append("; (" + features[i].getStatus() + ")");\r
+ sbuffer.append("; (" + features[i].getValue("status") + ")");\r
}\r
+ if (features[i].links != null)\r
+ sbuffer.append(" <img src=\"" + linkImageURL + "\">");\r
+\r
}\r
}\r
+ else if(features[i].begin==0 && features[i].end==0)\r
+ {\r
+ // seqSpecific.append(features[i].featureGroup+": "\r
+ // + features[i].getType()+" "\r
+ // +features[i].getDescription()+"<br>");\r
\r
+ }\r
}\r
\r
+ if(seqSpecific.length()>0)\r
+ seqSpecific.setLength(seqSpecific.length()-4);\r
+\r
+ sbuffer.append(seqSpecific);\r
sbuffer.append("</html>");\r
if(sbuffer.length()==13) // <html></html>\r
setToolTipText("");\r
}\r
}\r
\r
+ void setStatusMessage(SequenceI sequence, int res, int seq)\r
+ {\r
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
+ sequence.getName());\r
+\r
+ Object obj = null;\r
+ if (av.alignment.isNucleotide())\r
+ {\r
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
+ "");\r
+ if (obj != null)\r
+ text.append(" Nucleotide: ");\r
+ }\r
+ else\r
+ {\r
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
+ if (obj != null)\r
+ text.append(" Residue: ");\r
+ }\r
+\r
+ if (obj != null)\r
+ {\r
+\r
+ if (obj != "")\r
+ {\r
+ text.append(obj + " (" + sequence.findPosition(res) +\r
+ ")");\r
+ }\r
+ }\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public void mouseDragged(MouseEvent evt)\r
{\r
+ if (mouseWheelPressed)\r
+ {\r
+ int oldWidth = av.charWidth;\r
+\r
+ //Which is bigger, left-right or up-down?\r
+ if (Math.abs(evt.getY() - lastMousePress.getY())\r
+ > Math.abs(evt.getX() - lastMousePress.getX()))\r
+ {\r
+ int fontSize = av.font.getSize();\r
+\r
+ if (evt.getY() < lastMousePress.getY())\r
+ {\r
+ fontSize--;\r
+ }\r
+ else if (evt.getY() > lastMousePress.getY())\r
+ {\r
+ fontSize++;\r
+ }\r
+\r
+ if(fontSize<1)\r
+ fontSize = 1;\r
+\r
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));\r
+ av.charWidth = oldWidth;\r
+ ap.fontChanged();\r
+ }\r
+ else\r
+ {\r
+ if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)\r
+ {\r
+ av.charWidth--;\r
+ }\r
+ else if (evt.getX() > lastMousePress.getX())\r
+ {\r
+ av.charWidth++;\r
+ }\r
+\r
+ ap.repaint();\r
+ }\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ av.validCharWidth = fm.charWidth('M') <= av.charWidth;\r
+\r
+ lastMousePress = evt.getPoint();\r
+\r
+ return;\r
+ }\r
+\r
if (!editingSeqs)\r
{\r
doMouseDraggedDefineMode(evt);\r
return;\r
}\r
\r
- boolean dragRight = true;\r
-\r
- if ((res < av.getAlignment().getWidth()) && (res < lastres))\r
+ if ( (res < av.getAlignment().getWidth()) && (res < lastres))\r
{\r
- dragRight = false;\r
+ // dragLeft, delete gap\r
+ editSequence(false, res);\r
}\r
- else if(av.hasHiddenColumns)\r
+ else\r
+ editSequence(true, res);\r
+\r
+ mouseDragging = true;\r
+ if(scrollThread!=null)\r
+ scrollThread.setEvent(evt);\r
+\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
+\r
+ if (!groupEditing && av.hasHiddenRows)\r
{\r
- //Stop editing if the user has dragged beyond hiddenBoundary\r
- int lastCol = av.getColumnSelection().getHiddenRegionBoundary(lastres);\r
- if( lastCol < res)\r
+ if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
{\r
- if(lastres!=lastCol)\r
- {\r
- endEditing();\r
- return;\r
- }\r
+ groupEditing = true;\r
}\r
}\r
\r
- if(!groupEditing && av.hasHiddenRows)\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
+\r
+ //Are we editing within a selection group?\r
+ if (groupEditing\r
+ || (sg != null && sg.getSequences(true).contains(seq)))\r
{\r
- if(av.alignment.getSequenceAt(startseq).getHiddenSequences()!=null)\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
- groupEditing = 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
+\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 (res != lastres)\r
+ if(av.hasHiddenColumns )\r
{\r
- SequenceI seq;\r
- // Group editing\r
- if (groupEditing)\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
- SequenceGroup sg = av.getSelectionGroup();\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");\r
+ //Selection spans a hidden region\r
+ if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))\r
+ {\r
+ if(startres>=y2)\r
+ {\r
+ fixedLeft = y2;\r
+ }\r
+ else\r
+ {\r
+ fixedRight = y2 - 1;\r
+ }\r
+ }\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
- {\r
- sg = new SequenceGroup();\r
- sg.addSequence(av.alignment.getSequenceAt(startseq), false);\r
- }\r
\r
- SequenceGroup tmp = new SequenceGroup();\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\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
- //Do any of the sequences have hidden associates?\r
- for (int s = 0; s < sg.getSize(); s++)\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
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
+ for (int j = 0; j < startres - lastres; j++)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getCharAt(fixedRight - j)))\r
{\r
- seq = sg.getSequenceAt(s);\r
- tmp.addSequence(seq, false);\r
- if (seq.getHiddenSequences()!=null)\r
- {\r
- for(int h=0; h<seq.getHiddenSequences().getSize(); h++)\r
- tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),\r
- false);\r
- }\r
+ blank = false;\r
+ break;\r
}\r
-\r
- sg = tmp;\r
}\r
+ }\r
+ if (blank)\r
+ break;\r
+ }\r
\r
-\r
- if (sg == null)\r
+ if (!blank)\r
+ {\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
+ endEditing();\r
+ return;\r
}\r
\r
- int blankColumn = -1;\r
-\r
- // drag to right\r
- if (dragRight)\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 = alWidth+startres-lastres;\r
+ }\r
+ else\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ }\r
\r
- // Is it valid??\r
- // Find the next gap before the end\r
- // of the visible region boundary\r
- if (av.hasHiddenColumns)\r
- {\r
- if(res-lastres > 1)\r
- {\r
- res = lastres+1;\r
- }\r
-\r
-\r
- int lastCol = av.getColumnSelection().\r
- getHiddenRegionBoundary(res);\r
\r
- if(lastCol!=res)\r
- {\r
- for (blankColumn = lastCol;\r
- blankColumn > lastres;\r
- blankColumn--)\r
- {\r
- boolean blank = true;\r
- for (int s = 0; s < sg.getSize(); s++)\r
- {\r
- seq = sg.getSequenceAt(s);\r
-\r
- if (seq.getSequence().length() <= blankColumn)\r
- {\r
- continue;\r
- }\r
-\r
- if (!jalview.util.Comparison.isGap(\r
- seq.getSequence().charAt(blankColumn)))\r
- {\r
- blank = false;\r
- continue;\r
- }\r
- }\r
- if (blank)\r
- break;\r
- }\r
-\r
-\r
- if (blankColumn <= lastres)\r
- {\r
- endEditing();\r
- return;\r
- }\r
- }\r
- else\r
- blankColumn = -1;\r
+ // drag to left\r
+ else if(!insertGap)\r
+ {\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
\r
- }\r
+ for (int s = 0; s < sg.getSize(true); s++)\r
+ {\r
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
\r
- sg.setEndRes(sg.getEndRes() + (res - lastres));\r
+ for (int j = startres; j < lastres; j++)\r
+ {\r
+ if (seq.getSequence().length() <= j)\r
+ {\r
+ continue;\r
}\r
\r
- // drag to left\r
- else\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getSequence().charAt(j)))\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 = res; j < lastres; j++)\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
- }\r
- }\r
-\r
- if(res<sg.getStartRes())\r
- {\r
- sg.setStartRes(sg.getStartRes() - 1);\r
- }\r
- sg.setEndRes(sg.getEndRes() - (lastres - res));\r
+ // Not a gap, block edit not valid\r
+ endEditing();\r
+ return;\r
}\r
+ }\r
+ }\r
+ }\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- seq = sg.getSequenceAt(i);\r
\r
- // drag to right\r
- if (dragRight)\r
- {\r
- for (int j = lastres; j < res; j++)\r
- {\r
- insertChar(j, seq, blankColumn);\r
- }\r
- }\r
+ for (int i = 0; i < sg.getSize(true); i++)\r
+ {\r
+ seq = (SequenceI) sg.getSequences(true).elementAt(i);\r
\r
- // drag to left\r
- else\r
- {\r
- for (int j = res; j < lastres; j++)\r
- {\r
- if (seq.getLength()-1 > res)\r
- {\r
- deleteChar(res, seq);\r
- }\r
- }\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 /////Editing a single sequence///////////\r
+ else\r
{\r
- seq = av.alignment.getSequenceAt(startseq);\r
- if ((res < av.getAlignment().getWidth()) && (res > lastres))\r
+ // dragging to the left\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- // dragging to the right\r
- for (int j = lastres; j < res; j++)\r
- {\r
- insertChar(j, seq, j);\r
- }\r
+ deleteChar(startres, seq, fixedRight);\r
}\r
- else if ((res < av.getAlignment().getWidth()) &&\r
- (res < lastres))\r
+ else\r
{\r
- // dragging to the left\r
- for (int j = lastres; j > res; j--)\r
- {\r
- if (jalview.util.Comparison.isGap(\r
- av.alignment.getSequenceAt(startseq)\r
- .getSequence().charAt(res)))\r
- {\r
- deleteChar(res, seq);\r
- }\r
- else\r
- {\r
- break;\r
- }\r
- }\r
+ deleteChar(startres, seq);\r
}\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
- mouseDragging = true;\r
- if(scrollThread!=null)\r
- scrollThread.setEvent(evt);\r
-\r
- endEdit = res;\r
- lastres = res;\r
+ lastres = startres;\r
seqCanvas.repaint();\r
}\r
\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param j DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ void insertChar(int j, SequenceI seq)\r
+ {\r
+ seq.insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
+ }\r
+\r
+ void insertChar(int j, SequenceI seq, int fixedColumn)\r
+ {\r
+ //Find the next gap before the end of the visible region boundary\r
+ //If lastCol > j, theres a boundary after the gap insertion\r
+ int blankColumn = fixedColumn;\r
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
+ {\r
+ //Theres a space, so break and insert the gap\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (blankColumn <= j)\r
+ {\r
+ blankColumn = fixedColumn;\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
+ {\r
+ //Just Checking\r
+ System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));\r
+ return;\r
+ }\r
+\r
+ seq.deleteCharAt(blankColumn);\r
+ seq.insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
+ }\r
+\r
+ void deleteChar(int j, SequenceI seq, int fixedColumn)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+ {\r
+ ap.alignFrame.statusBar.setText(\r
+ "End editing: Tried removing residue " + seq.getCharAt(j));\r
+ return;\r
+ }\r
+\r
+ seq.deleteCharAt(j);\r
+ seq.insertCharAt(fixedColumn, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param j DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ void deleteChar(int j, SequenceI seq)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+ {\r
+ ap.alignFrame.statusBar.setText(\r
+ "End editing: Tried removing residue " + seq.getCharAt(j));\r
+ return;\r
+ }\r
+\r
+ seq.deleteCharAt(j);\r
+ seqEditOccurred = true;\r
+ seqCanvas.repaint();\r
+ }\r
/**\r
* DOCUMENT ME!\r
*\r
\r
public void mouseWheelMoved(MouseWheelEvent e)\r
{\r
- if (mouseWheelPressed)\r
+ e.consume();\r
+ /* if (mouseWheelPressed)\r
{\r
Font font = av.getFont();\r
int fontSize = font.getSize();\r
else if (fontSize > 1)\r
fontSize--;\r
\r
+\r
+\r
av.setFont(new Font(font.getName(), font.getStyle(), fontSize));\r
+\r
ap.fontChanged();\r
}\r
- else\r
+ else*/\r
{\r
if (e.getWheelRotation() > 0)\r
ap.scrollUp(false);\r
}\r
\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param j DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- */\r
- void insertChar(int j, SequenceI seq, int blankColumn)\r
- {\r
- if(av.hasHiddenColumns)\r
- {\r
- //Find the next gap before the end of the visible region boundary\r
- int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);\r
- if(lastCol != j)\r
- {\r
- if (!groupEditing || lastCol <= j)\r
- {\r
- blankColumn = lastCol;\r
- //If lastCol > j, theres a boundary after the gap insertion\r
- if (lastCol > j)\r
- {\r
- for (blankColumn = lastCol; blankColumn > j; blankColumn--)\r
- {\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
- {\r
- //Theres a space, so break and insert the gap\r
- break;\r
- }\r
- }\r
-\r
- if (blankColumn <= j)\r
- {\r
- endEditing();\r
- return;\r
- }\r
- }\r
-\r
- }\r
-\r
- // Editing with hidden regions only!!\r
- seq.deleteCharAt(blankColumn);\r
- }\r
- }\r
-\r
- seq.insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred = true;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param j DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- */\r
- public void deleteChar(int j, SequenceI seq)\r
- {\r
- if (av.hasHiddenColumns)\r
- {\r
- //Find the next gap before the end of the visible region boundary\r
- int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);\r
-\r
- //If lastCol > j, theres a boundary after the gap insertion\r
- if (lastCol > j)\r
- {\r
- seq.insertCharAt(lastCol, av.getGapCharacter());\r
- }\r
- }\r
-\r
- seq.deleteCharAt(j);\r
- seqEditOccurred = true;\r
-\r
- seqCanvas.repaint();\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
void editOccurred()\r
{\r
- if (endEdit == startEdit)\r
+ if (!seqEditOccurred)\r
{\r
ap.alignFrame.historyList.pop();\r
ap.alignFrame.updateEditMenuBar();\r
}\r
\r
+ endEditing();\r
+\r
av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
\r
}\r
"Cannot edit annotations in wrapped view.",\r
"Wrapped view - no edit",\r
JOptionPane.WARNING_MESSAGE);\r
- return;\r
+ return;\r
}\r
\r
if(seq<0 || res<0)\r
return;\r
\r
-\r
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
\r
if ((sequence == null) || (res > sequence.getLength()))\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
(allGroups[i].getEndRes() >= res))\r
{\r
stretchGroup = allGroups[i];\r
- av.setSelectionGroup(stretchGroup);\r
-\r
break;\r
}\r
}\r
}\r
+\r
+ av.setSelectionGroup(stretchGroup);\r
+\r
}\r
\r
- if (stretchGroup == null)\r
+\r
+ if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
{\r
- // define a new group here\r
- SequenceGroup sg = new SequenceGroup();\r
- sg.setStartRes(res);\r
- sg.setEndRes(res);\r
- sg.addSequence(sequence, false);\r
- av.setSelectionGroup(sg);\r
- stretchGroup = sg;\r
-\r
- if (av.getConservationSelected())\r
+ Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),\r
+ sequence.findPosition(res));\r
+ Vector links = new Vector();\r
+ for (int i = 0; i < allFeatures.size(); i++)\r
{\r
- SliderPanel.setConservationSlider(ap,\r
- av.getGlobalColourScheme(), "Background");\r
+ SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);\r
+ if (sf.links != null)\r
+ {\r
+ for (int j = 0; j < sf.links.size(); j++)\r
+ {\r
+ links.addElement(sf.links.elementAt(j));\r
+ }\r
+ }\r
}\r
\r
- if (av.getAbovePIDThreshold())\r
- {\r
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
- "Background");\r
- }\r
- }\r
- else if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
- {\r
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);\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
- // edit the properties of existing group\r
+ if (av.cursorMode)\r
+ {\r
+ seqCanvas.cursorX = findRes(evt);\r
+ seqCanvas.cursorY = findSeq(evt);\r
+ seqCanvas.repaint();\r
+ return;\r
}\r
\r
- if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
+ if (stretchGroup == null)\r
{\r
+ //Only if left mouse button do we want to change group sizes\r
+\r
+ // define a new group here\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ sg.addSequence(sequence, false);\r
+ av.setSelectionGroup(sg);\r
+ stretchGroup = sg;\r
+\r
+ if (av.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(ap,\r
+ av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
+\r
+ if (av.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
+ if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
+ {\r
// Edit end res position of selected group\r
changeEndRes = true;\r
- }\r
- else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))\r
- {\r
+ }\r
+ else if ( (stretchGroup != null) &&\r
+ (stretchGroup.getStartRes() == res))\r
+ {\r
// Edit end res position of selected group\r
changeStartRes = true;\r
+ }\r
+ stretchGroup.getWidth();\r
}\r
\r
- stretchGroup.getWidth();\r
-\r
seqCanvas.repaint();\r
}\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
+ if(res> av.alignment.getWidth())\r
{\r
- y = av.alignment.getHeight() -1;\r
+ res = av.alignment.getWidth()-1;\r
}\r
\r
if (stretchGroup.getEndRes() == res)\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
seqCanvas.repaint();\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
\r
// this class allows scrolling off the bottom of the visible alignment\r
\r
if (mouseDragging && (evt.getX() < 0))\r
{\r
- running = ap.scrollRight(true);\r
+ running = ap.scrollRight(false);\r
}\r
else if (mouseDragging && (evt.getX() >= getWidth()))\r
{\r
- running = ap.scrollRight(false);\r
+ running = ap.scrollRight(true);\r
}\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff