+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );\r
+ if(evt.getClickCount()>1)\r
+ {\r
+ if (av.getSelectionGroup().getSize(false) == 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
+ {\r
+ Font font = av.getFont();\r
+ int fontSize = font.getSize();\r
+ if (e.getWheelRotation() > 0 && fontSize < 51)\r
+ fontSize++;\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
+ {\r
+ if (e.getWheelRotation() > 0)\r
+ ap.scrollUp(false);\r
+ else\r
+ ap.scrollUp(true);\r
+ }\r
+\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void doMousePressedDefineMode(MouseEvent evt)\r
+ {\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
+ oldSeq = seq;\r
+\r
+ startWrapBlock=wrappedBlock;\r
+\r
+ if(av.wrapAlignment && seq>av.alignment.getHeight())\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Cannot edit annotations in wrapped view.",\r
+ "Wrapped view - no edit",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
+ if(seq<0 || res<0)\r
+ return;\r
+\r
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
+\r
+ if ((sequence == null) || (res > sequence.getLength()))\r
+ {\r
+ return;\r
+ }\r
+\r
+ stretchGroup = av.getSelectionGroup();\r
+\r
+ if (stretchGroup == null)\r
+ {\r
+ stretchGroup = av.alignment.findGroup(sequence);\r
+\r
+ if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&\r
+ (res < stretchGroup.getEndRes()))\r
+ {\r
+ av.setSelectionGroup(stretchGroup);\r
+ }\r
+ else\r
+ {\r
+ stretchGroup = null;\r
+ }\r
+ }\r
+ else if (!stretchGroup.getSequences(false).contains(sequence) ||\r
+ (stretchGroup.getStartRes() > res) ||\r
+ (stretchGroup.getEndRes() < res))\r
+ {\r
+ stretchGroup = null;\r
+\r
+ SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
+\r
+ if (allGroups != null)\r
+ {\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ {\r
+ if ((allGroups[i].getStartRes() <= res) &&\r
+ (allGroups[i].getEndRes() >= res))\r
+ {\r
+ stretchGroup = allGroups[i];\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
+ {\r
+ seqCanvas.cursorX = findRes(evt);\r
+ seqCanvas.cursorY = findSeq(evt);\r
+ seqCanvas.repaint();\r
+ return;\r
+ }\r
+\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) &&\r
+ (stretchGroup.getStartRes() == res))\r
+ {\r
+ // Edit end res position of selected group\r
+ changeStartRes = true;\r
+ }\r
+ stretchGroup.getWidth();\r
+ }\r
+\r
+ seqCanvas.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void doMouseReleasedDefineMode(MouseEvent evt)\r
+ {\r
+ if (stretchGroup == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+\r
+ if(stretchGroup.cs!=null)\r
+ {\r
+ if (stretchGroup.cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
+ stretchGroup.getSequences(true),\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
+ }\r
+ else\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
+ }\r
+ }\r
+ changeEndRes = false;\r
+ changeStartRes = false;\r
+ stretchGroup = null;\r
+\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void doMouseDraggedDefineMode(MouseEvent evt)\r
+ {\r
+ int res = findRes(evt);\r
+ int y = findSeq(evt);\r
+\r
+ if(wrappedBlock!=startWrapBlock)\r
+ return;\r
+\r
+ if (stretchGroup == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if(res>= av.alignment.getWidth())\r
+ {\r
+ res = av.alignment.getWidth()-1;\r
+ }\r
+\r
+ if (stretchGroup.getEndRes() == res)\r
+ {\r
+ // Edit end res position of selected group\r
+ changeEndRes = true;\r
+ }\r
+ else if (stretchGroup.getStartRes() == res)\r
+ {\r
+ // Edit start res position of selected group\r
+ changeStartRes = true;\r
+ }\r
+\r
+ if (res < av.getStartRes())\r
+ {\r
+ res = av.getStartRes();\r
+ }\r
+\r
+ if (changeEndRes)\r
+ {\r
+ if (res > (stretchGroup.getStartRes() - 1))\r
+ {\r
+ stretchGroup.setEndRes(res);\r
+ }\r
+ }\r
+ else if (changeStartRes)\r
+ {\r
+ if (res < (stretchGroup.getEndRes() + 1))\r
+ {\r
+ stretchGroup.setStartRes(res);\r
+ }\r
+ }\r
+\r
+ int dragDirection = 0;\r
+\r
+ if (y > oldSeq)\r
+ {\r
+ dragDirection = 1;\r
+ }\r
+ else if (y < oldSeq)\r
+ {\r
+ dragDirection = -1;\r
+ }\r
+\r
+\r
+ while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))\r
+ {\r
+ // This routine ensures we don't skip any sequences, as the\r
+ // selection is quite slow.\r
+ Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+\r
+ oldSeq += dragDirection;\r
+\r
+ if(oldSeq<0)\r
+ break;\r
+\r
+ Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+\r
+ if (stretchGroup.getSequences(false).contains(nextSeq))\r
+ {\r
+ stretchGroup.deleteSequence(seq, false);\r
+ }\r
+ else\r
+ {\r
+ if (seq != null)\r
+ {\r
+ stretchGroup.addSequence(seq, false);\r
+ }\r
+\r
+ stretchGroup.addSequence(nextSeq, false);\r
+ }\r
+ }\r
+\r
+ if(oldSeq < 0)\r
+ oldSeq = -1;\r
+\r
+ mouseDragging = true;\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.setEvent(evt);\r
+ }\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
+ class ScrollThread extends Thread\r
+ {\r
+ MouseEvent evt;\r
+ boolean running = false;\r
+\r
+ public ScrollThread()\r
+ {\r
+ start();\r
+ }\r
+\r
+ public void setEvent(MouseEvent e)\r
+ {\r
+ evt = e;\r
+ }\r
+\r
+ public void stopScrolling()\r
+ {\r
+ running = false;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ running = true;\r
+\r
+ while (running)\r
+ {\r
+ if (evt != null)\r
+ {\r
+ if (mouseDragging && (evt.getY() < 0) &&\r
+ (av.getStartSeq() > 0))\r
+ {\r
+ running = ap.scrollUp(true);\r
+ }\r
+\r
+ if (mouseDragging && (evt.getY() >= getHeight()) &&\r
+ (av.alignment.getHeight() > av.getEndSeq()))\r
+ {\r
+ running = ap.scrollUp(false);\r
+ }\r
+\r
+ if (mouseDragging && (evt.getX() < 0))\r
+ {\r
+ running = ap.scrollRight(false);\r
+ }\r
+ else if (mouseDragging && (evt.getX() >= getWidth()))\r
+ {\r
+ running = ap.scrollRight(true);\r
+ }\r
+ }\r
+\r
+ try\r
+ {\r
+ Thread.sleep(20);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ }\r
+ }\r
+}\r