/*\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
StringBuffer keyboardNo1;\r
StringBuffer keyboardNo2;\r
\r
+ java.net.URL linkImageURL;\r
+\r
/**\r
* Creates a new SeqPanel object.\r
*\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
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
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
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
int fontSize = av.font.getSize();\r
\r
- if (evt.getY() < lastMousePress.getY() && av.charHeight > 1)\r
+ if (evt.getY() < lastMousePress.getY())\r
{\r
fontSize--;\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
}\r
else\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
"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
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
+\r
+ if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
+ {\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
+ 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
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+ return;\r
}\r
\r
if (av.cursorMode)\r
return;\r
}\r
\r
-\r
if (stretchGroup == null)\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(), "Background");\r
- }\r
+ //Only if left mouse button do we want to change group sizes\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
- pop.show(this, evt.getX(), evt.getY());\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
- // edit the properties of existing group\r
- }\r
+ if (av.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(ap,\r
+ av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
\r
- if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))\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
- {\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