/*\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
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
-\r
+import jalview.commands.EditCommand;\r
import jalview.schemes.*;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
-\r
import javax.swing.*;\r
+import java.util.Vector;\r
\r
\r
/**\r
MouseMotionListener, MouseWheelListener\r
\r
{\r
- /** DOCUMENT ME!! */\r
- public SeqCanvas seqCanvas;\r
-\r
- /** DOCUMENT ME!! */\r
- public AlignmentPanel ap;\r
- protected int lastres;\r
- protected int startseq;\r
- protected AlignViewport av;\r
-\r
- // if character is inserted or deleted, we will need to recalculate the conservation\r
- boolean seqEditOccurred = false;\r
- ScrollThread scrollThread = null;\r
- boolean mouseDragging = false;\r
- boolean editingSeqs = false;\r
- boolean groupEditing = false;\r
-\r
- //////////////////////////////////////////\r
- /////Everything below this is for defining the boundary of the rubberband\r
- //////////////////////////////////////////\r
- int oldSeq = -1;\r
- boolean changeEndSeq = false;\r
- boolean changeStartSeq = false;\r
- boolean changeEndRes = false;\r
- boolean changeStartRes = false;\r
- SequenceGroup stretchGroup = null;\r
- boolean remove = false;\r
-\r
- boolean mouseWheelPressed = false;\r
- StringBuffer keyboardNo1;\r
- StringBuffer keyboardNo2;\r
-\r
- /**\r
- * Creates a new SeqPanel object.\r
- *\r
- * @param avp DOCUMENT ME!\r
- * @param p DOCUMENT ME!\r
- */\r
- public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
+ /** DOCUMENT ME!! */\r
+ public SeqCanvas seqCanvas;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public AlignmentPanel ap;\r
+ protected int lastres;\r
+ protected int startseq;\r
+ protected AlignViewport av;\r
+\r
+ ScrollThread scrollThread = null;\r
+ boolean mouseDragging = false;\r
+ boolean editingSeqs = false;\r
+ boolean groupEditing = false;\r
+\r
+ //////////////////////////////////////////\r
+ /////Everything below this is for defining the boundary of the rubberband\r
+ //////////////////////////////////////////\r
+ int oldSeq = -1;\r
+ boolean changeEndSeq = false;\r
+ boolean changeStartSeq = false;\r
+ boolean changeEndRes = false;\r
+ boolean changeStartRes = false;\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
+ StringBuffer tooltipText = new StringBuffer("<html>");\r
+ String tmpString;\r
+\r
+ EditCommand editCommand;\r
+\r
+ /**\r
+ * Creates a new SeqPanel object.\r
+ *\r
+ * @param avp DOCUMENT ME!\r
+ * @param p DOCUMENT ME!\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
+ this.av = avp;\r
+ setBackground(Color.white);\r
+\r
+ seqCanvas = new SeqCanvas(avp);\r
+ setLayout(new BorderLayout());\r
+ add(seqCanvas, BorderLayout.CENTER);\r
+\r
+ ap = p;\r
+\r
+ if (!av.isDataset())\r
{\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- ToolTipManager.sharedInstance().setInitialDelay(0);\r
- ToolTipManager.sharedInstance().setDismissDelay(10000);\r
- this.av = avp;\r
- setBackground(Color.white);\r
-\r
- seqCanvas = new SeqCanvas(avp);\r
- setLayout(new BorderLayout());\r
- add(seqCanvas, BorderLayout.CENTER);\r
-\r
- ap = p;\r
-\r
- if(!av.isDataset())\r
- {\r
- addMouseMotionListener(this);\r
- addMouseListener(this);\r
- addMouseWheelListener(this);\r
- }\r
+ addMouseMotionListener(this);\r
+ addMouseListener(this);\r
+ addMouseWheelListener(this);\r
}\r
+ }\r
\r
- int startWrapBlock=-1;\r
- int wrappedBlock=-1;\r
- int findRes(MouseEvent evt)\r
- {\r
- int res = 0;\r
- int x = evt.getX();\r
+ int startWrapBlock = -1;\r
+ int wrappedBlock = -1;\r
+ int findRes(MouseEvent evt)\r
+ {\r
+ int res = 0;\r
+ int x = evt.getX();\r
\r
if (av.wrapAlignment)\r
{\r
int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ hgap + seqCanvas.getAnnotationHeight();\r
\r
- int y = evt.getY();\r
- y -= hgap;\r
- x -= seqCanvas.LABEL_WEST;\r
-\r
+ int y = evt.getY();\r
+ y -= hgap;\r
+ x -= seqCanvas.LABEL_WEST;\r
\r
- int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());\r
+ int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());\r
+ if (cwidth < 1)\r
+ return 0;\r
\r
- wrappedBlock = y / cHeight;\r
- wrappedBlock += av.getStartRes() / cwidth;\r
+ wrappedBlock = y / cHeight;\r
+ wrappedBlock += av.getStartRes() / cwidth;\r
\r
- res = wrappedBlock * cwidth + x / av.getCharWidth();\r
+ res = wrappedBlock * cwidth + x / av.getCharWidth();\r
\r
}\r
else\r
{\r
- res = (x / av.getCharWidth()) + av.getStartRes();\r
+ res = (x / av.getCharWidth()) + av.getStartRes();\r
}\r
\r
- if(av.hasHiddenColumns)\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ if (av.hasHiddenColumns)\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
\r
return res;\r
\r
- }\r
+ }\r
\r
- int findSeq(MouseEvent evt)\r
- {\r
+ int findSeq(MouseEvent evt)\r
+ {\r
+ int seq = 0;\r
+ int y = evt.getY();\r
\r
- int seq = 0;\r
- int y = evt.getY();\r
+ if (av.wrapAlignment)\r
+ {\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- if (av.wrapAlignment)\r
- {\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap + seqCanvas.getAnnotationHeight();\r
\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight\r
- + hgap + seqCanvas.getAnnotationHeight();\r
+ y -= hgap;\r
\r
- y -= hgap;\r
+ seq = Math.min( (y % cHeight) / av.getCharHeight(),\r
+ av.alignment.getHeight() - 1);\r
+ }\r
+ else\r
+ {\r
+ seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),\r
+ av.alignment.getHeight() - 1);\r
+ }\r
\r
- seq = ( (y % cHeight) / av.getCharHeight());\r
- }\r
- else\r
+ return seq;\r
+ }\r
+\r
+ SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)\r
+ {\r
+ Vector tmp = new Vector();\r
+ SequenceFeature[] features = sequence.getSequenceFeatures();\r
+ if (features != null)\r
+ {\r
+ for (int i = 0; i < features.length; i++)\r
+ {\r
+ if (av.featuresDisplayed == null\r
+ || !av.featuresDisplayed.containsKey(features[i].getType()))\r
+ continue;\r
+\r
+ if ( (features[i].getBegin() <= res) &&\r
+ (features[i].getEnd() >= res))\r
+ {\r
+ tmp.addElement(features[i]);\r
+ }\r
+ }\r
+ }\r
+\r
+ features = new SequenceFeature[tmp.size()];\r
+ for(int i=0; i<tmp.size(); i++)\r
+ {\r
+ features[i] = (SequenceFeature)tmp.elementAt(i);\r
+ }\r
+\r
+ return features;\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
- seq = (y / av.getCharHeight()) + av.getStartSeq();\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
-\r
- return seq;\r
- }\r
+ return allFeatures;\r
+ }\r
\r
void endEditing()\r
{\r
+ if (editCommand!=null && editCommand.getSize() > 0)\r
+ {\r
+ ap.alignFrame.addHistoryItem(editCommand);\r
+ av.firePropertyChange("alignment", null,\r
+ av.getAlignment().getSequences());\r
+ }\r
+\r
startseq = -1;\r
lastres = -1;\r
- seqEditOccurred = false;\r
editingSeqs = false;\r
groupEditing = false;\r
keyboardNo1 = null;\r
keyboardNo2 = null;\r
+ editCommand = null;\r
}\r
\r
void setCursorRow()\r
{\r
seqCanvas.cursorX += dx;\r
seqCanvas.cursorY += dy;\r
+ if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))\r
+ {\r
+ int original = seqCanvas.cursorX - dx;\r
+ int maxWidth = av.alignment.getWidth();\r
+\r
+ while(!av.colSel.isVisible(seqCanvas.cursorX)\r
+ && seqCanvas.cursorX<maxWidth\r
+ && seqCanvas.cursorX>0)\r
+ {\r
+ seqCanvas.cursorX += dx;\r
+ }\r
+\r
+ if(seqCanvas.cursorX>=maxWidth\r
+ || !av.colSel.isVisible(seqCanvas.cursorX) )\r
+ {\r
+ seqCanvas.cursorX = original;\r
+ }\r
+ }\r
+\r
scrollToVisible();\r
}\r
\r
\r
\r
endEditing();\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
- while (seqCanvas.cursorX < av.startRes)\r
+ if(av.wrapAlignment)\r
{\r
- if(!ap.scrollRight(false))\r
- break;\r
+ ap.scrollToWrappedVisible(seqCanvas.cursorX);\r
}\r
- while (seqCanvas.cursorX > av.endRes)\r
+ else\r
{\r
- if(!ap.scrollRight(true))\r
- break;\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.colSel.adjustForHiddenColumns(av.startRes))\r
+ {\r
+ if (!ap.scrollRight(false))\r
+ break;\r
+ }\r
+ while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))\r
+ {\r
+ if (!ap.scrollRight(true))\r
+ break;\r
+ }\r
+ }\r
}\r
-\r
setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),\r
seqCanvas.cursorX, seqCanvas.cursorY);\r
\r
else\r
{\r
// Now add any sequences between min and max\r
- sg.sequences.clear();\r
+ sg.getSequences(null).clear();\r
for (int i = min; i < max; i++)\r
{\r
sg.addSequence(av.alignment.getSequenceAt(i), false);\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
+ endEditing();\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
+ endEditing();\r
}\r
\r
void numberPressed(char value)\r
return;\r
}\r
\r
- editOccurred();\r
-\r
endEditing();\r
+\r
ap.repaint();\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
return;\r
}\r
\r
-\r
-\r
int seq = findSeq(evt);\r
int res = findRes(evt);\r
\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
\r
setStatusMessage(sequence, res, seq);\r
\r
+\r
+\r
+ tooltipText.setLength(6); // Cuts the buffer back to <html>\r
+\r
+ SequenceGroup [] groups = av.alignment.findAllGroups(sequence);\r
+ if(groups!=null)\r
+ {\r
+ for(int g=0; g<groups.length; g++)\r
+ {\r
+ if(groups[g].getStartRes()<=res && groups[g].getEndRes()>=res)\r
+ {\r
+ if (!groups[g].getName().startsWith("JTreeGroup") &&\r
+ !groups[g].getName().startsWith("JGroup"))\r
+ tooltipText.append(groups[g].getName() + " ");\r
+\r
+ if(groups[g].getDescription()!=null)\r
+ tooltipText.append(groups[g].getDescription()+"<BR>");\r
+ }\r
+ }\r
+ }\r
+\r
+\r
// use aa to see if the mouse pointer is on a\r
if (av.showSequenceFeatures)\r
{\r
- SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();\r
- if(features!=null)\r
- {\r
- StringBuffer sbuffer = new StringBuffer("<html>");\r
+ SequenceFeature[] features = findFeaturesAtRes(\r
+ sequence.getDatasetSequence(), sequence.findPosition(res));\r
\r
- for (int i = 0; i < features.length; i++)\r
+ if (features != null)\r
+ {\r
+ for (int i = 0; i < features.length; i++)\r
+ {\r
+ if (features[i].getType().equals("disulfide bond"))\r
{\r
-\r
- if ( (features[i].getBegin() <= sequence.findPosition(res)) &&\r
- (features[i].getEnd() >= sequence.findPosition(res)))\r
+ if (features[i].getBegin() == sequence.findPosition(res)\r
+ || features[i].getEnd() == sequence.findPosition(res))\r
{\r
- if(av.featuresDisplayed==null\r
- || !av.featuresDisplayed.containsKey(features[i].getType()))\r
- continue;\r
+ if (tooltipText.length() > 6)\r
+ tooltipText.append("<br>");\r
+ tooltipText.append("disulfide bond " + features[i].getBegin() + ":" +\r
+ features[i].getEnd());\r
+ if (features[i].links != null)\r
+ tooltipText.append(" <img src=\"" + linkImageURL + "\">");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (tooltipText.length() > 6)\r
+ tooltipText.append("<br>");\r
\r
+ tooltipText.append(features[i].getType() + " " +\r
+ features[i].begin);\r
+ if (features[i].begin != features[i].end)\r
+ tooltipText.append(" " + features[i].end);\r
\r
- if (features[i].getType().equals("disulfide bond"))\r
+ if (features[i].getDescription() != null\r
+ && !features[i].description.equals(features[i].getType()))\r
+ {\r
+ tmpString = features[i].getDescription();\r
+ int startTag = tmpString.toUpperCase().indexOf("<HTML>");\r
+ if (startTag > -1)\r
{\r
- if (features[i].getBegin() == sequence.findPosition(res)\r
- || features[i].getEnd() == sequence.findPosition(res))\r
- {\r
- if (sbuffer.length() > 6)\r
- sbuffer.append("<br>");\r
- sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +\r
- features[i].getEnd());\r
- }\r
+ tmpString = tmpString.substring(startTag + 6);\r
}\r
- else\r
+ int endTag = tmpString.toUpperCase().indexOf("</BODY>");\r
+ if (endTag > -1)\r
+ {\r
+ tmpString = tmpString.substring(0, endTag);\r
+ }\r
+ endTag = tmpString.toUpperCase().indexOf("</HTML>");\r
+ if (endTag > -1)\r
{\r
- if (sbuffer.length() > 6)\r
- sbuffer.append("<br>");\r
- if(features[i].featureGroup!=null)\r
- sbuffer.append(features[i].featureGroup+";");\r
+ tmpString = tmpString.substring(0, endTag);\r
+ }\r
\r
- sbuffer.append(features[i].getType());\r
+ if (startTag > -1)\r
+ {\r
+ tooltipText.append("; " + tmpString);\r
+ }\r
+ else\r
+ {\r
+ if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)\r
+ {\r
+ //The description does not specify html is to\r
+ //be used, so we must remove < > symbols\r
+ tmpString = tmpString.replaceAll("<", "<");\r
+ tmpString = tmpString.replaceAll(">", ">");\r
\r
- if (features[i].getDescription() != null\r
- && !features[i].description.equals(features[i].getType()))\r
- sbuffer.append("; " + features[i].getDescription());\r
+ tooltipText.append("; ");\r
+ tooltipText.append(tmpString);\r
\r
- if (features[i].getStatus() != null && features[i].getStatus().length()>0)\r
- {\r
- sbuffer.append("; (" + features[i].getStatus() + ")");\r
}\r
+ else\r
+ tooltipText.append("; " + tmpString);\r
}\r
}\r
+ if (features[i].getValue("status") != null)\r
+ {\r
+ String status = features[i].getValue("status").toString();\r
+ if (status.length() > 0)\r
+ tooltipText.append("; (" + features[i].getValue("status") + ")");\r
+ }\r
\r
- }\r
+ if (features[i].links != null)\r
+ tooltipText.append(" <img src=\"" + linkImageURL + "\">");\r
\r
- sbuffer.append("</html>");\r
- if(sbuffer.length()==13) // <html></html>\r
- setToolTipText("");\r
- else\r
- setToolTipText(sbuffer.toString());\r
+ }\r
}\r
- else\r
- setToolTipText("");\r
+ }\r
}\r
+ if (tooltipText.length() == 6) // <html></html>\r
+ {\r
+ setToolTipText(null);\r
+ }\r
+ else\r
+ {\r
+ tooltipText.append("</html>");\r
+ setToolTipText(tooltipText.toString());\r
+ }\r
+ // else\r
+ // setToolTipText(null);\r
}\r
\r
void setStatusMessage(SequenceI sequence, int res, int seq)\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
boolean fixedColumns = false;\r
SequenceGroup sg = av.getSelectionGroup();\r
\r
- if(groupEditing && sg==null)\r
- return;\r
+ SequenceI seq = av.alignment.getSequenceAt(startseq);\r
\r
+ //No group, but the sequence may represent a group\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
+ if (av.hiddenRepSequences!=null\r
+ && av.hiddenRepSequences.containsKey(seq))\r
{\r
+ sg = (SequenceGroup)av.hiddenRepSequences.get(seq);\r
groupEditing = true;\r
}\r
}\r
\r
- SequenceI seq = av.alignment.getSequenceAt(startseq);\r
+\r
StringBuffer message = new StringBuffer();\r
if (groupEditing)\r
- message.append("Edit group:");\r
+ {\r
+ message.append("Edit group:");\r
+ if (editCommand == null)\r
+ editCommand = new EditCommand("Edit Group");\r
+ }\r
else\r
- message.append("Edit sequence: "+seq.getName());\r
+ {\r
+ message.append("Edit sequence: " + seq.getName());\r
+ String label = seq.getName();\r
+ if(label.length()>10)\r
+ label = label.substring(0,10);\r
+ if(editCommand==null)\r
+ editCommand = new EditCommand("Edit "+label);\r
+ }\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(av.hiddenRepSequences).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 = (SequenceGroup) av.hiddenRepSequences.get(seq);\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
+ 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(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
\r
- sg = tmp;\r
- }*/\r
- // int blankColumn = -1;\r
\r
+ if (groupEditing)\r
+ {\r
+ Vector vseqs = sg.getSequences(av.hiddenRepSequences);\r
+ int g, groupSize = vseqs.size();\r
+ SequenceI[] groupSeqs = new SequenceI[groupSize];\r
+ for (g = 0; g < groupSeqs.length; g++)\r
+ groupSeqs[g] = (SequenceI) vseqs.elementAt(g);\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
+\r
+ for (g = 0; g < groupSize; g++)\r
{\r
- seq = sg.getSequenceAt(s);\r
for (int j = 0; j < startres - lastres; j++)\r
{\r
if (!jalview.util.Comparison.isGap(\r
- seq.getCharAt(fixedRight - j)))\r
+ groupSeqs[g].getCharAt(fixedRight - j)))\r
{\r
blank = false;\r
break;\r
\r
if (!blank)\r
{\r
- if(sg.getSize() == av.alignment.getHeight())\r
+ if(sg.getSize() == 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()+1+startres-lastres);\r
- fixedRight = av.alignment.getWidth()+startres-lastres;\r
+ sg.setEndRes(sg.getEndRes()+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 (g = 0; g < groupSize; g++)\r
{\r
- seq = sg.getSequenceAt(s);\r
-\r
for (int j = startres; j < lastres; j++)\r
{\r
- if (seq.getSequence().length() <= j)\r
+ if (groupSeqs[g].getLength() <= j)\r
{\r
continue;\r
}\r
\r
if (!jalview.util.Comparison.isGap(\r
- seq.getSequence().charAt(j)))\r
+ groupSeqs[g].getCharAt(j)))\r
{\r
// Not a gap, block edit not valid\r
endEditing();\r
}\r
}\r
\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- seq = sg.getSequenceAt(i);\r
-\r
if (insertGap)\r
{\r
// dragging to the right\r
- for (int j = lastres; j < startres; j++)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j < startres; j++)\r
{\r
- insertChar(j, seq, fixedRight);\r
+ insertChar(j, groupSeqs, fixedRight);\r
}\r
- else\r
- insertChar(j, seq);\r
+ }\r
+ else\r
+ {\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ groupSeqs,\r
+ startres, startres-lastres,\r
+ av.alignment,\r
+ true);\r
}\r
}\r
else\r
{\r
// dragging to the left\r
- for (int j = lastres; j > startres; j--)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j > startres; j--)\r
{\r
- deleteChar(startres, seq, fixedRight);\r
- }\r
- else\r
- {\r
- deleteChar(startres, seq);\r
+ deleteChar(startres, groupSeqs, fixedRight);\r
}\r
}\r
+ else\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ groupSeqs,\r
+ startres, lastres - startres,\r
+ av.alignment,\r
+ true);\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
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j < startres; j++)\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, new SequenceI[]{seq}, fixedRight);\r
}\r
- else\r
- insertChar(j, seq);\r
+ }\r
+ else\r
+ {\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ new SequenceI[]\r
+ {seq},\r
+ lastres, startres-lastres,\r
+ av.alignment,\r
+ true);\r
}\r
}\r
else\r
{\r
// dragging to the left\r
- for (int j = lastres; j > startres; j--)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j > startres; j--)\r
{\r
- deleteChar(startres, seq, fixedRight);\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))\r
+ {\r
+ endEditing();\r
+ break;\r
+ }\r
+ deleteChar(startres, new SequenceI[]{seq}, fixedRight);\r
}\r
- else\r
+ }\r
+ else\r
+ {\r
+ //could be a keyboard edit trying to delete none gaps\r
+ int max=0;\r
+ for(int m = startres; m<lastres; m++)\r
{\r
- deleteChar(startres, seq);\r
+ if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))\r
+ break;\r
+ max++;\r
+ }\r
+\r
+ if (max>0)\r
+ {\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ new SequenceI[]\r
+ {seq},\r
+ startres, max,\r
+ av.alignment,\r
+ true);\r
}\r
}\r
}\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
+ 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
+ for(int s=0; s<seq.length; s++)\r
{\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\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
+\r
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
{\r
- //Theres a space, so break and insert the gap\r
- break;\r
+ if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))\r
+ {\r
+ //Theres a space, so break and insert the gap\r
+ break;\r
+ }\r
}\r
- }\r
\r
- if (blankColumn <= j)\r
- {\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
+ if (blankColumn <= j)\r
+ {\r
+ blankColumn = fixedColumn;\r
+ endEditing();\r
+ return;\r
+ }\r
}\r
\r
- seq.deleteCharAt(blankColumn);\r
- seq.insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred = true;\r
- }\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ seq,\r
+ blankColumn, 1, av.alignment, true);\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
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ seq,\r
+ j, 1, av.alignment,\r
+ true);\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
+ 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
- seqEditOccurred = true;\r
- seqCanvas.repaint();\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ seq,\r
+ j, 1, av.alignment, true);\r
+\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ seq,\r
+ fixedColumn, 1, av.alignment, true);\r
}\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
}\r
\r
public void mouseClicked(MouseEvent evt)\r
- {}\r
+ {\r
+ SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );\r
+ if(evt.getClickCount()>1)\r
+ {\r
+ if (av.getSelectionGroup().getSize() == 1\r
+ && av.getSelectionGroup().getEndRes()\r
+ - av.getSelectionGroup().getStartRes() < 2)\r
+ av.setSelectionGroup(null);\r
+\r
+ SequenceFeature[] features = findFeaturesAtRes(\r
+ sequence.getDatasetSequence(),\r
+ sequence.findPosition( findRes(evt) )\r
+ );\r
+\r
+ if(features!=null && features.length>0)\r
+ {\r
+ SearchResults highlight = new SearchResults();\r
+ highlight.addResult(sequence,\r
+ features[0].getBegin(),\r
+ features[0].getEnd());\r
+ seqCanvas.highlightSearchResults(highlight);\r
+ }\r
+ if(features!=null && features.length>0)\r
+ {\r
+ seqCanvas.getFeatureRenderer().amendFeatures(\r
+ new SequenceI[]\r
+ {sequence}, features, false, ap);\r
+\r
+ seqCanvas.highlightSearchResults(null);\r
+ }\r
+ }\r
+ }\r
\r
public void mouseWheelMoved(MouseWheelEvent e)\r
{\r
e.consume();\r
- if (mouseWheelPressed)\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- void editOccurred()\r
- {\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
-\r
/**\r
* DOCUMENT ME!\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(null).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(av.hiddenRepSequences),\r
stretchGroup.getWidth());\r
}\r
\r
+ if (stretchGroup.cs instanceof Blosum62ColourScheme\r
+ || stretchGroup.cs instanceof PIDColourScheme\r
+ || stretchGroup.cs.conservationApplied()\r
+ || stretchGroup.cs.getThreshold()>0)\r
+ stretchGroup.recalcConservation();\r
+\r
if (stretchGroup.cs.conservationApplied())\r
{\r
SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
stretchGroup.getName());\r
- stretchGroup.recalcConservation();\r
}\r
else\r
{\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
- PaintRefresher.Refresh(av.alignment);\r
+\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
}\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
+ if(res>= av.alignment.getWidth())\r
{\r
res = av.alignment.getWidth()-1;\r
}\r
\r
Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
\r
- if (stretchGroup.sequences.contains(nextSeq))\r
+ if (stretchGroup.getSequences(null).contains(nextSeq))\r
{\r
stretchGroup.deleteSequence(seq, false);\r
}\r
git://source.jalview.org / jalview.git / blobdiff