+ //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
+ 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
+ //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
+\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
+ // 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
+ blank = false;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if (blank)\r
+ break;\r
+ }\r
+\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
+ }\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 = 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 s = 0; s < sg.getSize(true); s++)\r
+ {\r
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
+\r
+ for (int j = startres; 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
+\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
+ 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
+ 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
+\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
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseEntered(MouseEvent e)\r
+ {\r
+ if(oldSeq < 0)\r
+ oldSeq = 0;\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseExited(MouseEvent e)\r
+ {\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (mouseDragging)\r
+ {\r
+ scrollThread = new ScrollThread();\r
+ }\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\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
+ /**\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
+ * @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.conservationApplied())\r
+ {\r
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
+ stretchGroup.getName());\r
+ stretchGroup.recalcConservation();\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
+ PaintRefresher.Refresh(av.alignment);\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