-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-\r
-public class SeqPanel\r
- extends Panel implements MouseMotionListener, MouseListener\r
-{\r
-\r
- public SeqCanvas seqCanvas;\r
- public AlignmentPanel ap;\r
-\r
- protected int lastres;\r
- protected int startseq;\r
- int startEdit = -1;\r
- int endEdit = -1;\r
-\r
- protected AlignViewport av;\r
-\r
- // if character is inserted or deleted, we will need to recalculate the conservation\r
- int seqEditOccurred = -1;\r
-\r
- ScrollThread scrollThread = null;\r
- boolean mouseDragging = false;\r
-\r
- boolean editingSeqs = false;\r
- boolean groupEditing = false;\r
-\r
- public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
- {\r
- this.av = avp;\r
-\r
- seqCanvas = new SeqCanvas(avp);\r
- setLayout(new BorderLayout());\r
- add(seqCanvas);\r
-\r
- ap = p;\r
-\r
- seqCanvas.addMouseMotionListener(this);\r
- seqCanvas.addMouseListener(this);\r
-\r
- seqCanvas.repaint();\r
- }\r
-\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
- {\r
- if (evt.isAltDown() || evt.isControlDown())\r
- {\r
- groupEditing = true;\r
- }\r
-\r
- editingSeqs = true;\r
- doMousePressed(evt);\r
- }\r
- else\r
- {\r
- doMousePressedDefineMode(evt);\r
- }\r
- }\r
-\r
- public void mouseClicked(MouseEvent evt){}\r
-\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if (!editingSeqs)\r
- {\r
- doMouseReleasedDefineMode(evt);\r
- return;\r
- }\r
-\r
-\r
- if (seqEditOccurred > -1)\r
- {\r
- editOccurred(seqEditOccurred);\r
- }\r
-\r
- startseq = -1;\r
- lastres = -1;\r
- seqEditOccurred = -1;\r
- editingSeqs = false;\r
- groupEditing = false;\r
- ap.repaint();\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
-\r
- if (av.wrapAlignment)\r
- {\r
-\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\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
-\r
- int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);\r
-\r
- wrappedBlock = y / cHeight;\r
- wrappedBlock += av.getStartRes() / cwidth;\r
-\r
- res = wrappedBlock * cwidth + x / av.getCharWidth();\r
-\r
- }\r
- else\r
- {\r
- res = (x / av.getCharWidth()) + av.getStartRes();\r
- }\r
-\r
- return res;\r
-\r
- }\r
-\r
- int findSeq(MouseEvent evt)\r
- {\r
-\r
- int seq = 0;\r
- int y = evt.getY();\r
-\r
- if (av.wrapAlignment)\r
- {\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
-\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight\r
- + hgap + seqCanvas.getAnnotationHeight();\r
-\r
- y -= hgap;\r
-\r
- seq = ( (y % cHeight) / av.getCharHeight());\r
- }\r
- else\r
- {\r
- seq = (y / av.getCharHeight()) + av.getStartSeq();\r
- }\r
-\r
- return seq;\r
- }\r
-\r
-\r
- public void doMousePressed(MouseEvent evt)\r
- {\r
- ap.alignFrame.addHistoryItem(new HistoryItem(\r
- "Edit Sequence", av.alignment, HistoryItem.EDIT));\r
-\r
- int seq = findSeq(evt);\r
- int res = findRes(evt);\r
-\r
- if (seq < av.getAlignment().getHeight() &&\r
- res < av.getAlignment().getSequenceAt(seq).getLength())\r
- {\r
- //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);\r
- // Find the residue's position in the sequence (res is the position\r
- // in the alignment\r
-\r
- startseq = seq;\r
- lastres = res;\r
- }\r
- else\r
- {\r
- startseq = -1;\r
- lastres = -1;\r
- }\r
-\r
- return;\r
- }\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- int res = findRes(evt);\r
- int seq = findSeq(evt);\r
-\r
- if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)\r
- {\r
- return;\r
- }\r
-\r
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
- if (res > sequence.getLength())\r
- {\r
- return;\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
- if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
- {\r
- seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
- }\r
-\r
-\r
- // use aa to see if the mouse pointer is on a\r
- if (av.showSequenceFeatures\r
- && sequence.getSequenceFeatures()!=null\r
- && av.featuresDisplayed!=null)\r
- {\r
- int index = 0;\r
- sequence.getSequenceFeatures();\r
- boolean first = true;\r
- while (index < sequence.getSequenceFeatures().length)\r
- {\r
- SequenceFeature sf = sequence.getSequenceFeatures()[index];\r
- if (sf.getBegin() <= sequence.findPosition(res) &&\r
- sf.getEnd() >= sequence.findPosition(res))\r
- {\r
- if(!av.featuresDisplayed.containsKey(sf.getType()))\r
- {\r
- index++;\r
- continue;\r
- }\r
-\r
- if(first)\r
- {\r
- text.append(" Sequence Feature:");\r
- first = false;\r
- }\r
-\r
- text.append(" "+sf.getType());\r
-\r
- if(sf.getDescription()!=null)\r
- text.append(" "+sf.getDescription());\r
-\r
- if (sf.getStatus()!=null && sf.getStatus().length() > 0)\r
- {\r
- text.append(" (" + sf.getStatus() + ")");\r
- }\r
- text.append("; ");\r
- }\r
-\r
- index++;\r
-\r
- }\r
- }\r
-\r
- ap.alignFrame.statusBar.setText(text.toString());\r
-\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- if (!editingSeqs)\r
- {\r
- doMouseDraggedDefineMode(evt);\r
- return;\r
- }\r
-\r
- // If we're dragging we're editing\r
- int res = findRes(evt);\r
- if (res < 0)\r
- {\r
- res = 0;\r
- }\r
-\r
- if (lastres == -1 || lastres == res)\r
- {\r
- return;\r
- }\r
-\r
- boolean dragRight = true;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
- {\r
- dragRight = false;\r
- }\r
-\r
- if (res != lastres)\r
- {\r
- // Group editing\r
- if (groupEditing)\r
- {\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if (sg == null)\r
- {\r
- lastres = -1;\r
- return;\r
- }\r
-\r
- // drag to right\r
- if (dragRight)\r
- {\r
- sg.setEndRes(sg.getEndRes() + (res - lastres));\r
- }\r
-\r
- // drag to left\r
- else\r
- {\r
- /// Are we able to delete?\r
- // ie are all columns blank?\r
- boolean deleteAllowed = false;\r
- for (int s = 0; s < sg.getSize(); s++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(s);\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(seq.getSequence().charAt(j)))\r
- {\r
- // Not a gap, block edit not valid\r
- res = j + 1;\r
- deleteAllowed = false;\r
- continue;\r
- }\r
- deleteAllowed = true;\r
- }\r
- }\r
-\r
- if (!deleteAllowed)\r
- {\r
- lastres = -1;\r
- return;\r
- }\r
-\r
- sg.setEndRes(sg.getEndRes() - (lastres - res));\r
- }\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI s = sg.getSequenceAt(i);\r
- int k = av.alignment.findIndex(s);\r
-\r
- // drag to right\r
- if (dragRight)\r
- {\r
- for (int j = lastres; j < res; j++)\r
- {\r
- insertChar(j, k);\r
- }\r
- }\r
-\r
- // drag to left\r
- else\r
- {\r
- for (int j = res; j < lastres; j++)\r
- {\r
- if (s.getLength() > j)\r
- {\r
- deleteChar(res, k);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- else /////Editing a single sequence///////////\r
- {\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
- {\r
- // dragging to the right\r
- for (int j = lastres; j < res; j++)\r
- {\r
- insertChar(j, startseq);\r
- }\r
- }\r
- else if (res < av.getAlignment().getWidth() && res < lastres)\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).getSequence().charAt(res)))\r
- {\r
-\r
- deleteChar(res, startseq);\r
- }\r
- else\r
- {\r
- if(scrollThread!=null)\r
- {\r
- scrollThread.running = false;\r
- scrollThread = null;\r
- }\r
- break;\r
- }\r
- }\r
- }\r
-\r
- }\r
- }\r
-\r
- mouseDragging = true;\r
- if (res > av.endRes || res < av.startRes)\r
- {\r
- mouseExited(evt);\r
- }\r
-\r
- if (scrollThread != null)\r
- scrollThread.setEvent(evt);\r
-\r
-\r
- endEdit = res;\r
- lastres = res;\r
- seqCanvas.repaint();\r
- }\r
-\r
- public void insertChar(int j, int seq)\r
- {\r
- av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred = seq;\r
- }\r
-\r
- public void deleteChar(int j, int seq)\r
- {\r
-\r
- av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
- seqEditOccurred = seq;\r
- av.alignment.getWidth();\r
- repaint();\r
- }\r
-\r
- void editOccurred(int i)\r
- {\r
- if (endEdit == startEdit)\r
- {\r
- ap.alignFrame.historyList.pop();\r
- ap.alignFrame.updateEditMenuBar();\r
- }\r
-\r
- av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
- }\r
-\r
-//////////////////////////////////////////\r
-/////Everything below this is for defining the boundary of the rubberband\r
-//////////////////////////////////////////\r
- int oldSeq = -1;\r
- public void doMousePressedDefineMode(MouseEvent evt)\r
- {\r
- if (scrollThread != null)\r
- {\r
- scrollThread.running = false;\r
- scrollThread = null;\r
- }\r
-\r
- int res = findRes(evt);\r
- int seq = findSeq(evt);\r
- oldSeq = seq;\r
- startWrapBlock=wrappedBlock;\r
-\r
- if(seq==-1)\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
- 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
-\r
- else if (!stretchGroup.sequences.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
- av.setSelectionGroup(stretchGroup);\r
- break;\r
- }\r
- }\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, av.getGlobalColourScheme(),\r
- "Background");\r
- }\r
- if (av.getAbovePIDThreshold())\r
- {\r
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
- "Background");\r
- }\r
-\r
- }\r
-\r
- // DETECT RIGHT MOUSE BUTTON IN AWT\r
- else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
- InputEvent.BUTTON3_MASK)\r
- {\r
- APopupMenu popup = new APopupMenu(ap, null, null);\r
- this.add(popup);\r
- popup.show(this, evt.getX(), evt.getY());\r
- }\r
-\r
- if (stretchGroup != null && stretchGroup.getEndRes() == res)\r
- {\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
- }\r
-\r
- else if (stretchGroup != null && stretchGroup.getStartRes() == res)\r
- {\r
- // Edit end res position of selected group\r
- changeStartRes = true;\r
- }\r
-\r
- }\r
-\r
- boolean changeEndSeq = false;\r
- boolean changeStartSeq = false;\r
- boolean changeEndRes = false;\r
- boolean changeStartRes = false;\r
- SequenceGroup stretchGroup = null;\r
-\r
- public void doMouseReleasedDefineMode(MouseEvent evt)\r
- {\r
- if (stretchGroup == null)\r
- {\r
- return;\r
- }\r
-\r
- if(stretchGroup.cs!=null)\r
- {\r
- if (stretchGroup.cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
- sequences,\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
- ap.repaint();\r
- }\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
- mouseDragging = true;\r
-\r
-\r
- if(y > av.alignment.getHeight())\r
- {\r
- y = av.alignment.getHeight() -1;\r
- }\r
-\r
- if(res>av.alignment.getWidth())\r
- res = av.alignment.getWidth()-1;\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 < 0)\r
- {\r
- res = 0;\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.sequences.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
-\r
- if(res>av.endRes || res<av.startRes\r
- || y<av.startSeq || y>av.endSeq)\r
- {\r
- mouseExited(evt);\r
- }\r
-\r
- if (scrollThread != null)\r
- {\r
- scrollThread.setEvent(evt);\r
- }\r
-\r
- seqCanvas.repaint();\r
- }\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
- public void mouseExited(MouseEvent e)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
-\r
- if (mouseDragging && scrollThread==null)\r
- {\r
- scrollThread = new ScrollThread();\r
- }\r
- }\r
-\r
- // this class allows scrolling off the bottom of the visible alignment\r
- class ScrollThread\r
- extends Thread\r
- {\r
- MouseEvent evt;\r
- boolean running = false;\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
- while (running)\r
- {\r
-\r
- if (evt != null)\r
- {\r
-\r
- if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
- {\r
- running = ap.scrollUp(true);\r
- }\r
-\r
- if (mouseDragging && evt.getY() >= getSize().height &&\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(true);\r
- }\r
-\r
- else if (mouseDragging && evt.getX() >= getSize().width)\r
- {\r
- running = ap.scrollRight(false);\r
- }\r
- }\r
-\r
- try\r
- {\r
- Thread.sleep(75);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+import java.util.Vector;
+
+public class SeqPanel
+ extends Panel implements MouseMotionListener, MouseListener
+{
+
+ public SeqCanvas seqCanvas;
+ public AlignmentPanel ap;
+
+ protected int lastres;
+ protected int startseq;
+
+ protected AlignViewport av;
+
+ // if character is inserted or deleted, we will need to recalculate the conservation
+ boolean seqEditOccurred = false;
+
+ ScrollThread scrollThread = null;
+ boolean mouseDragging = false;
+ boolean editingSeqs = false;
+ boolean groupEditing = false;
+
+ int oldSeq = -1;
+ boolean changeEndSeq = false;
+ boolean changeStartSeq = false;
+ boolean changeEndRes = false;
+ boolean changeStartRes = false;
+ SequenceGroup stretchGroup = null;
+
+ StringBuffer keyboardNo1;
+ StringBuffer keyboardNo2;
+
+ boolean mouseWheelPressed = false;
+ Point lastMousePress;
+
+ public SeqPanel(AlignViewport avp, AlignmentPanel p)
+ {
+ this.av = avp;
+
+ seqCanvas = new SeqCanvas(avp);
+ setLayout(new BorderLayout());
+ add(seqCanvas);
+
+ ap = p;
+
+ seqCanvas.addMouseMotionListener(this);
+ seqCanvas.addMouseListener(this);
+
+ seqCanvas.repaint();
+ }
+
+ void endEditing()
+ {
+ startseq = -1;
+ lastres = -1;
+ seqEditOccurred = false;
+ editingSeqs = false;
+ groupEditing = false;
+ keyboardNo1 = null;
+ keyboardNo2 = null;
+ }
+
+ void setCursorRow()
+ {
+ seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
+ scrollToVisible();
+ }
+
+ void setCursorColumn()
+ {
+ seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
+ scrollToVisible();
+ }
+
+ void setCursorRowAndColumn()
+ {
+ if(keyboardNo2==null)
+ {
+ keyboardNo2 = new StringBuffer();
+ }
+ else
+ {
+ seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+ seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
+ scrollToVisible();
+ }
+ }
+
+ void setCursorPosition()
+ {
+ SequenceI sequence =
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+ seqCanvas.cursorX = sequence.findIndex(
+ getKeyboardNo(keyboardNo1)-1
+ );
+ scrollToVisible();
+ }
+
+ void moveCursor(int dx, int dy)
+ {
+ seqCanvas.cursorX += dx;
+ seqCanvas.cursorY += dy;
+ scrollToVisible();
+ }
+
+ void scrollToVisible()
+ {
+ if (seqCanvas.cursorX < 0)
+ seqCanvas.cursorX = 0;
+ else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+ seqCanvas.cursorX = av.alignment.getWidth() - 1;
+
+ if (seqCanvas.cursorY < 0)
+ seqCanvas.cursorY = 0;
+ else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+ seqCanvas.cursorY = av.alignment.getHeight() - 1;
+
+
+ endEditing();
+ if (av.wrapAlignment)
+ {
+ ap.scrollToWrappedVisible(seqCanvas.cursorX);
+ }
+ else
+ {
+ while (seqCanvas.cursorY < av.startSeq)
+ {
+ ap.scrollUp(true);
+ }
+ while (seqCanvas.cursorY + 1 > av.endSeq)
+ {
+ ap.scrollUp(false);
+ }
+ while (seqCanvas.cursorX < av.startRes)
+ {
+
+ if (!ap.scrollRight(false))
+ break;
+ }
+ while (seqCanvas.cursorX > av.endRes)
+ {
+ if (!ap.scrollRight(true))
+ break;
+ }
+ }
+ setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ seqCanvas.cursorX, seqCanvas.cursorY);
+
+ seqCanvas.repaint();
+ }
+
+ void setSelectionAreaAtCursor(boolean topLeft)
+ {
+ SequenceI sequence =
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+ if(av.getSelectionGroup()!=null)
+ {
+ SequenceGroup sg = av.selectionGroup;
+ //Find the top and bottom of this group
+ int min = av.alignment.getHeight(), max = 0;
+ for(int i=0; i<sg.getSize(false); i++)
+ {
+ int index = av.alignment.findIndex( sg.getSequenceAt(i) );
+ if(index > max)
+ max = index;
+ if(index < min)
+ min = index;
+ }
+
+ max ++;
+
+ if(topLeft)
+ {
+ sg.setStartRes(seqCanvas.cursorX);
+ if(sg.getEndRes()<seqCanvas.cursorX)
+ sg.setEndRes(seqCanvas.cursorX);
+
+ min = seqCanvas.cursorY;
+ }
+ else
+ {
+ sg.setEndRes(seqCanvas.cursorX);
+ if(sg.getStartRes()>seqCanvas.cursorX)
+ sg.setStartRes(seqCanvas.cursorX);
+
+ max = seqCanvas.cursorY+1;
+ }
+
+ if(min>max)
+ {
+ // Only the user can do this
+ av.setSelectionGroup(null);
+ }
+ else
+ {
+ // Now add any sequences between min and max
+ sg.getSequences(false).removeAllElements();
+ for (int i = min; i < max; i++)
+ {
+ sg.addSequence(av.alignment.getSequenceAt(i), false);
+ }
+ }
+ }
+
+ if (av.getSelectionGroup() == null)
+ {
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(seqCanvas.cursorX);
+ sg.setEndRes(seqCanvas.cursorX);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ }
+
+
+ ap.repaint();
+ }
+
+ void insertGapAtCursor(boolean group)
+ {
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+ av.alignment, HistoryItem.EDIT));
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
+ editOccurred();
+ }
+
+ void deleteGapAtCursor(boolean group)
+ {
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+ av.alignment, HistoryItem.EDIT));
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
+ editSequence(false, seqCanvas.cursorX);
+ editOccurred();
+ }
+
+ void numberPressed(char value)
+ {
+ if(keyboardNo1==null)
+ keyboardNo1 = new StringBuffer();
+
+ if(keyboardNo2!=null)
+ keyboardNo2.append(value);
+ else
+ keyboardNo1.append(value);
+ }
+
+ int getKeyboardNo(StringBuffer kb)
+ {
+ if(kb==null)
+ return 1;
+ else
+ return Integer.parseInt(kb.toString());
+ }
+
+ void setStatusMessage(SequenceI sequence, int res, int seq)
+ {
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+ sequence.getName());
+
+ Object obj = null;
+ if (av.alignment.isNucleotide())
+ {
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+ "");
+ if (obj != null)
+ text.append(" Nucleotide: ");
+ }
+ else
+ {
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ if (obj != null)
+ text.append(" Residue: ");
+ }
+
+ if (obj != null)
+ {
+
+ if (obj != "")
+ {
+ text.append(obj + " (" + sequence.findPosition(res) +
+ ")");
+ }
+ }
+
+ ap.alignFrame.statusBar.setText(text.toString());
+
+ }
+ public void mousePressed(MouseEvent evt)
+ {
+ lastMousePress = evt.getPoint();
+
+ if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
+ InputEvent.BUTTON2_MASK && !av.MAC)
+ {
+ mouseWheelPressed = true;
+ return;
+ }
+
+ if (evt.isShiftDown() || evt.isControlDown())
+ {
+ if (evt.isControlDown())
+ {
+ groupEditing = true;
+ }
+ editingSeqs = true;
+ }
+ else
+ {
+ doMousePressedDefineMode(evt);
+ return;
+ }
+
+
+ int seq = findSeq(evt);
+ int res = findRes(evt);
+
+ if(seq<0 || res<0)
+ return;
+
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+ av.alignment, HistoryItem.EDIT));
+
+ if ((seq < av.getAlignment().getHeight()) &&
+ (res < av.getAlignment().getSequenceAt(seq).getLength()))
+ {
+ startseq = seq;
+ lastres = res;
+ }
+ else
+ {
+ startseq = -1;
+ lastres = -1;
+ }
+
+ return;
+ }
+
+ public void mouseClicked(MouseEvent evt){}
+
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ mouseDragging = false;
+ mouseWheelPressed = false;
+
+ if (!editingSeqs)
+ {
+ doMouseReleasedDefineMode(evt);
+ return;
+ }
+
+ editOccurred();
+
+ endEditing();
+ ap.repaint();
+ }
+
+ int startWrapBlock=-1;
+ int wrappedBlock=-1;
+ int findRes(MouseEvent evt)
+ {
+ int res = 0;
+ int x = evt.getX();
+
+ if (av.wrapAlignment)
+ {
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ hgap += av.charHeight;
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight
+ + hgap + seqCanvas.getAnnotationHeight();
+
+ int y = evt.getY();
+ y -= hgap;
+ x -= seqCanvas.LABEL_WEST;
+
+
+ int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
+
+ wrappedBlock = y / cHeight;
+ wrappedBlock += av.getStartRes() / cwidth;
+
+ res = wrappedBlock * cwidth + x / av.getCharWidth();
+
+ }
+ else
+ {
+ res = (x / av.getCharWidth()) + av.getStartRes();
+ }
+
+ if(av.hasHiddenColumns)
+ res = av.getColumnSelection().adjustForHiddenColumns(res);
+
+ return res;
+
+ }
+
+ int findSeq(MouseEvent evt)
+ {
+
+ int seq = 0;
+ int y = evt.getY();
+
+ if (av.wrapAlignment)
+ {
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ hgap += av.charHeight;
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight
+ + hgap + seqCanvas.getAnnotationHeight();
+
+ y -= hgap;
+
+ seq = Math.min( (y % cHeight) / av.getCharHeight(),
+ av.alignment.getHeight() -1);
+ if(seq<0)
+ seq = 0;
+ }
+ else
+ {
+ seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+ av.alignment.getHeight() -1);
+ if(seq<0)
+ seq = 0;
+ }
+
+ return seq;
+ }
+
+
+ public void doMousePressed(MouseEvent evt)
+ {
+ ap.alignFrame.addHistoryItem(new HistoryItem(
+ "Edit Sequence", av.alignment, HistoryItem.EDIT));
+
+ int seq = findSeq(evt);
+ int res = findRes(evt);
+
+ if (seq < av.getAlignment().getHeight() &&
+ res < av.getAlignment().getSequenceAt(seq).getLength())
+ {
+ //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
+ // Find the residue's position in the sequence (res is the position
+ // in the alignment
+
+ startseq = seq;
+ lastres = res;
+ }
+ else
+ {
+ startseq = -1;
+ lastres = -1;
+ }
+
+ return;
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+
+ if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
+ {
+ return;
+ }
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ if (res > sequence.getLength())
+ {
+ return;
+ }
+
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+ sequence.getName());
+
+ Object obj = null;
+ if (av.alignment.isNucleotide())
+ {
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+ "");
+ if(obj!=null)
+ text.append(" Nucleotide: ");
+ }
+ else
+ {
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ if(obj!=null)
+ text.append(" Residue: ");
+ }
+
+ if (obj != null)
+ {
+ if (obj != "")
+ {
+ text.append(obj + " (" + sequence.findPosition(res) + ")");
+ }
+ }
+
+ if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+ {
+ seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+ }
+
+ ap.alignFrame.statusBar.setText(text.toString());
+
+
+ // use aa to see if the mouse pointer is on a
+ if (av.showSequenceFeatures
+ && sequence.getSequenceFeatures()!=null
+ && av.featuresDisplayed!=null)
+ {
+ StringBuffer featureText = new StringBuffer();
+ Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
+
+ int index = 0;
+ while (index < allFeatures.size())
+ {
+ SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
+
+ featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);
+
+ if (sf.getDescription() != null)
+ featureText.append(" " + sf.getDescription());
+
+ if (sf.getValue("status") != null )
+ {
+ featureText.append(" (" + sf.getValue("status") + ")");
+ }
+ featureText.append("\n");
+
+ index++;
+ }
+
+
+ if (tooltip == null)
+ tooltip = new Tooltip(featureText.toString(), seqCanvas);
+ else
+ tooltip.setTip(featureText.toString());
+
+ tooltip.repaint();
+
+ }
+ }
+
+ Vector getAllFeaturesAtRes(SequenceI seq, int res)
+ {
+ Vector allFeatures = new Vector();
+ int index = 0;
+ if(seq.getSequenceFeatures()!=null)
+ {
+ while (index < seq.getSequenceFeatures().length)
+ {
+ SequenceFeature sf = seq.getSequenceFeatures()[index];
+ if (sf.getBegin() <= res &&
+ sf.getEnd() >= res)
+ {
+ if (av.featuresDisplayed.containsKey(sf.getType()))
+ {
+ allFeatures.addElement(sf);
+ }
+ }
+ index++;
+ }
+ }
+ return allFeatures;
+ }
+
+ Tooltip tooltip;
+
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (mouseWheelPressed)
+ {
+ int oldWidth = av.charWidth;
+
+ //Which is bigger, left-right or up-down?
+ if (Math.abs(evt.getY() - lastMousePress.y)
+ > Math.abs(evt.getX() - lastMousePress.x))
+ {
+ int fontSize = av.font.getSize();
+
+ if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+ {
+ fontSize--;
+ }
+ else if (evt.getY() > lastMousePress.y)
+ {
+ fontSize++;
+ }
+
+
+ if(fontSize<1)
+ fontSize = 1;
+
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+ av.charWidth = oldWidth;
+ }
+ else
+ {
+ if (evt.getX() < lastMousePress.x && av.charWidth > 1)
+ {
+ av.charWidth--;
+ }
+ else if (evt.getX() > lastMousePress.x)
+ {
+ av.charWidth++;
+ }
+
+ if(av.charWidth<1)
+ {
+ av.charWidth = 1;
+ }
+ }
+
+ ap.fontChanged();
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+ lastMousePress = evt.getPoint();
+
+ ap.repaint();
+ ap.annotationPanel.image = null;
+ return;
+ }
+
+ if (!editingSeqs)
+ {
+ doMouseDraggedDefineMode(evt);
+ return;
+ }
+
+ int res = findRes(evt);
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ if ((lastres == -1) || (lastres == res))
+ {
+ return;
+ }
+
+ if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+ {
+ // dragLeft, delete gap
+ editSequence(false, res);
+ }
+ else
+ editSequence(true, res);
+
+ mouseDragging = true;
+ if(scrollThread!=null)
+ scrollThread.setEvent(evt);
+
+ }
+
+ synchronized void editSequence(boolean insertGap, int startres)
+ {
+ int fixedLeft = -1;
+ int fixedRight = -1;
+ boolean fixedColumns = false;
+ SequenceGroup sg = av.getSelectionGroup();
+
+
+ if (!groupEditing && av.hasHiddenRows)
+ {
+ if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
+ {
+ groupEditing = true;
+ }
+ }
+
+ //No group, but the sequence may represent a group
+ if (groupEditing
+ && sg == null
+ && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
+ {
+ groupEditing = false;
+ }
+
+ SequenceI seq = av.alignment.getSequenceAt(startseq);
+ StringBuffer message = new StringBuffer();
+ if (groupEditing)
+ message.append("Edit group:");
+ else
+ message.append("Edit sequence: "+seq.getName());
+
+ if(insertGap)
+ message.append(" insert ");
+ else
+ message.append(" delete ");
+
+ message.append(Math.abs(startres-lastres)+" gaps.");
+ ap.alignFrame.statusBar.setText(message.toString());
+
+
+ //Are we editing within a selection group?
+ if (groupEditing
+ || (sg != null && sg.getSequences(true).contains(seq)))
+ {
+ fixedColumns = true;
+
+ //sg might be null as the user may only see 1 sequence,
+ //but the sequence represents a group
+ if (sg == null)
+ {
+ sg = new SequenceGroup(null, null, false, false, false, 0,
+ av.alignment.getWidth()-1);
+ sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+ }
+
+ fixedLeft = sg.getStartRes();
+ fixedRight = sg.getEndRes();
+
+ if ( (startres < fixedLeft && lastres >= fixedLeft)
+ || (startres >= fixedLeft && lastres < fixedLeft)
+ || (startres > fixedRight && lastres <=fixedRight)
+ || (startres <= fixedRight && lastres > fixedRight))
+ {
+ endEditing();
+ return;
+ }
+
+ if (fixedLeft > startres)
+ {
+ fixedRight = fixedLeft - 1;
+ fixedLeft = 0;
+ }
+ else if (fixedRight < startres)
+ {
+ fixedLeft = fixedRight;
+ fixedRight = -1;
+ }
+ }
+
+
+ if(av.hasHiddenColumns )
+ {
+ fixedColumns = true;
+ int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+ int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+
+ if ( (insertGap && startres > y1 && lastres < y1)
+ || (!insertGap && startres < y2 && lastres > y2))
+ {
+ endEditing();
+ return;
+ }
+
+ //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+ //Selection spans a hidden region
+ if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
+ {
+ if(startres>=y2)
+ {
+ fixedLeft = y2;
+ }
+ else
+ {
+ fixedRight = y2 - 1;
+ }
+ }
+ }
+
+
+ if (groupEditing)
+ {
+ // drag to right
+ if (insertGap)
+ {
+ //If the user has selected the whole sequence, and is dragging to
+ // the right, we can still extend the alignment and selectionGroup
+ if( sg.getStartRes() == 0
+ && sg.getEndRes() == fixedRight
+ && sg.getEndRes() == av.alignment.getWidth()-1
+ )
+ {
+ sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ fixedRight = sg.getEndRes();
+ }
+
+ // Is it valid with fixed columns??
+ // Find the next gap before the end
+ // of the visible region boundary
+ boolean blank = false;
+ for (fixedRight = fixedRight;
+ fixedRight > lastres;
+ fixedRight--)
+ {
+ blank = true;
+ for (int s = 0; s < sg.getSize(true); s++)
+ {
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);
+ for (int j = 0; j < startres - lastres; j++)
+ {
+ if (!jalview.util.Comparison.isGap(
+ seq.getCharAt(fixedRight - j)))
+ {
+ blank = false;
+ break;
+ }
+ }
+ }
+ if (blank)
+ break;
+ }
+
+ if (!blank)
+ {
+ if(sg.getSize(false) == av.alignment.getHeight() )
+ {
+ if((av.hasHiddenColumns
+ && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
+ {
+ endEditing();
+ return;
+ }
+
+ int alWidth = av.alignment.getWidth();
+ if(av.hasHiddenRows)
+ {
+ int hwidth = av.alignment.getHiddenSequences().getWidth();
+ if(hwidth>alWidth)
+ alWidth = hwidth;
+ }
+ //We can still insert gaps if the selectionGroup
+ //contains all the sequences
+ sg.setEndRes(sg.getEndRes()+startres-lastres);
+ fixedRight = alWidth+startres-lastres;
+ }
+ else
+ {
+ endEditing();
+ return;
+ }
+ }
+ }
+
+
+ // drag to left
+ else if(!insertGap)
+ {
+ /// Are we able to delete?
+ // ie are all columns blank?
+
+ for (int s = 0; s < sg.getSize(true); s++)
+ {
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);
+
+ for (int j = startres; j < lastres; j++)
+ {
+ if (seq.getSequence().length() <= j)
+ {
+ continue;
+ }
+
+ if (!jalview.util.Comparison.isGap(
+ seq.getSequence().charAt(j)))
+ {
+ // Not a gap, block edit not valid
+ endEditing();
+ return;
+ }
+ }
+ }
+ }
+
+
+ for (int i = 0; i < sg.getSize(true); i++)
+ {
+ seq = (SequenceI) sg.getSequences(true).elementAt(i);
+
+ if (insertGap)
+ {
+ // dragging to the right
+ for (int j = lastres; j < startres; j++)
+ {
+ if (fixedColumns && fixedRight != -1)
+ {
+ insertChar(j, seq, fixedRight);
+ }
+ else
+ insertChar(j, seq);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ for (int j = lastres; j > startres; j--)
+ {
+ if (fixedColumns && fixedRight != -1)
+ {
+ deleteChar(startres, seq, fixedRight);
+ }
+ else
+ {
+ deleteChar(startres, seq);
+ }
+ }
+ }
+ }
+ }
+ else /////Editing a single sequence///////////
+ {
+ if (insertGap)
+ {
+ // dragging to the right
+ for (int j = lastres; j < startres; j++)
+ {
+ if (fixedColumns && fixedRight != -1)
+ {
+ insertChar(j, seq, fixedRight);
+ }
+ else
+ insertChar(j, seq);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ for (int j = lastres; j > startres; j--)
+ {
+ if (fixedColumns && fixedRight != -1)
+ {
+ deleteChar(startres, seq, fixedRight);
+ }
+ else
+ {
+ deleteChar(startres, seq);
+ }
+ }
+ }
+ }
+
+ lastres = startres;
+ seqCanvas.repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param j DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ */
+ void insertChar(int j, SequenceI seq)
+ {
+ seq.insertCharAt(j, av.getGapCharacter());
+ seqEditOccurred = true;
+ }
+
+ void insertChar(int j, SequenceI seq, int fixedColumn)
+ {
+ //Find the next gap before the end of the visible region boundary
+ //If lastCol > j, theres a boundary after the gap insertion
+ int blankColumn = fixedColumn;
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
+ {
+ //Theres a space, so break and insert the gap
+ break;
+ }
+ }
+
+ if (blankColumn <= j)
+ {
+ endEditing();
+ return;
+ }
+
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
+ {
+ //Just Checking
+ System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
+ return;
+ }
+
+ seq.deleteCharAt(blankColumn);
+ seq.insertCharAt(j, av.getGapCharacter());
+ seqEditOccurred = true;
+ }
+
+ void deleteChar(int j, SequenceI seq, int fixedColumn)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+ {
+ ap.alignFrame.statusBar.setText(
+ "End editing: Tried removing residue " + seq.getCharAt(j));
+ return;
+ }
+
+ seq.deleteCharAt(j);
+ seq.insertCharAt(fixedColumn, av.getGapCharacter());
+ seqEditOccurred = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param j DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ */
+ void deleteChar(int j, SequenceI seq)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+ {
+ ap.alignFrame.statusBar.setText(
+ "End editing: Tried removing residue " + seq.getCharAt(j));
+ return;
+ }
+
+ seq.deleteCharAt(j);
+ seqEditOccurred = true;
+ seqCanvas.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i DOCUMENT ME!
+ */
+ void editOccurred()
+ {
+ if (!seqEditOccurred)
+ {
+ ap.alignFrame.historyList.pop();
+ ap.alignFrame.updateEditMenuBar();
+ }
+
+ endEditing();
+
+ av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
+
+ }
+
+//////////////////////////////////////////
+/////Everything below this is for defining the boundary of the rubberband
+//////////////////////////////////////////
+ public void doMousePressedDefineMode(MouseEvent evt)
+ {
+
+
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+ oldSeq = seq;
+ startWrapBlock=wrappedBlock;
+
+ if(seq==-1)
+ return;
+
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+
+ if (sequence == null || res > sequence.getLength())
+ {
+ return;
+ }
+
+ stretchGroup = av.getSelectionGroup();
+
+ if (stretchGroup == null)
+ {
+ stretchGroup = av.alignment.findGroup(sequence);
+ if (stretchGroup != null && res > stretchGroup.getStartRes() &&
+ res < stretchGroup.getEndRes())
+ {
+ av.setSelectionGroup(stretchGroup);
+ }
+ else
+ {
+ stretchGroup = null;
+ }
+ }
+
+ else if (!stretchGroup.getSequences(false).contains(sequence)
+ || stretchGroup.getStartRes() > res
+ || stretchGroup.getEndRes() < res)
+ {
+ stretchGroup = null;
+
+ SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+
+ if (allGroups != null)
+ {
+ for (int i = 0; i < allGroups.length; i++)
+ {
+ if (allGroups[i].getStartRes() <= res &&
+ allGroups[i].getEndRes() >= res)
+ {
+ stretchGroup = allGroups[i];
+ break;
+ }
+ }
+ }
+ av.setSelectionGroup(stretchGroup);
+ }
+
+
+ // DETECT RIGHT MOUSE BUTTON IN AWT
+ if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
+ InputEvent.BUTTON3_MASK)
+ {
+ Vector allFeatures = getAllFeaturesAtRes(sequence,
+ sequence.findPosition(res));
+
+ Vector links = null;
+ if(allFeatures!=null)
+ {
+ for (int i = 0; i < allFeatures.size(); i++)
+ {
+ SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
+ if (sf.links != null)
+ {
+ links = new Vector();
+ for (int j = 0; j < sf.links.size(); j++)
+ {
+ links.addElement(sf.links.elementAt(j));
+ }
+ }
+ }
+ }
+ APopupMenu popup = new APopupMenu(ap, null, links);
+ this.add(popup);
+ popup.show(this, evt.getX(), evt.getY());
+ ap.repaint();
+ return;
+ }
+
+ if (av.cursorMode)
+ {
+ seqCanvas.cursorX = findRes(evt);
+ seqCanvas.cursorY = findSeq(evt);
+ seqCanvas.repaint();
+ return;
+ }
+
+ //Only if left mouse button do we want to change group sizes
+
+ if (stretchGroup == null)
+ {
+ // define a new group here
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(res);
+ sg.setEndRes(res);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ stretchGroup = sg;
+
+ if (av.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+ "Background");
+ }
+ if (av.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+ "Background");
+ }
+
+ }
+ }
+
+ public void doMouseReleasedDefineMode(MouseEvent evt)
+ {
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ if(stretchGroup.cs!=null)
+ {
+ if (stretchGroup.cs instanceof ClustalxColourScheme)
+ {
+ ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+ stretchGroup.getSequences(true),
+ stretchGroup.getWidth());
+ }
+
+ if (stretchGroup.cs.conservationApplied())
+ {
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ stretchGroup.recalcConservation();
+ }
+ else
+ {
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ }
+ }
+ changeEndRes = false;
+ changeStartRes = false;
+ stretchGroup = null;
+ PaintRefresher.Refresh(av.alignment);
+ ap.repaint();
+ }
+
+ public void doMouseDraggedDefineMode(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int y = findSeq(evt);
+
+ if(wrappedBlock!=startWrapBlock)
+ return;
+
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ mouseDragging = true;
+
+
+ if(y > av.alignment.getHeight())
+ {
+ y = av.alignment.getHeight() -1;
+ }
+
+ if(res>av.alignment.getWidth())
+ res = av.alignment.getWidth()-1;
+
+ if (stretchGroup.getEndRes() == res)
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if (stretchGroup.getStartRes() == res)
+ {
+ // Edit start res position of selected group
+ changeStartRes = true;
+ }
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ if (changeEndRes)
+ {
+ if (res > (stretchGroup.getStartRes() - 1))
+ {
+ stretchGroup.setEndRes(res);
+ }
+ }
+ else if (changeStartRes)
+ {
+ if (res < (stretchGroup.getEndRes() + 1))
+ {
+ stretchGroup.setStartRes(res);
+ }
+ }
+
+ int dragDirection = 0;
+
+ if (y > oldSeq)
+ {
+ dragDirection = 1;
+ }
+ else if (y < oldSeq)
+ {
+ dragDirection = -1;
+ }
+
+
+ while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+ {
+ // This routine ensures we don't skip any sequences, as the
+ // selection is quite slow.
+ Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+ oldSeq += dragDirection;
+
+ if(oldSeq<0)
+ break;
+
+ Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+ if (stretchGroup.getSequences(false).contains(nextSeq))
+ {
+ stretchGroup.deleteSequence(seq, false);
+ }
+ else
+ {
+ if (seq != null)
+ {
+ stretchGroup.addSequence(seq, false);
+ }
+
+ stretchGroup.addSequence(nextSeq, false);
+ }
+ }
+
+ if(oldSeq < 0)
+ oldSeq = -1;
+
+
+ if(res>av.endRes || res<av.startRes
+ || y<av.startSeq || y>av.endSeq)
+ {
+ mouseExited(evt);
+ }
+
+ if (scrollThread != null)
+ {
+ scrollThread.setEvent(evt);
+ }
+
+ seqCanvas.repaint();
+ }
+
+ public void mouseEntered(MouseEvent e)
+ {
+ if (oldSeq < 0)
+ oldSeq = 0;
+
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+ }
+
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging && scrollThread==null)
+ {
+ scrollThread = new ScrollThread();
+ }
+ }
+
+ void scrollCanvas(MouseEvent evt)
+ {
+ if(evt==null)
+ {
+ if(scrollThread!=null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+ mouseDragging = false;
+ }
+ else
+ {
+ if (scrollThread == null)
+ scrollThread = new ScrollThread();
+
+ mouseDragging = true;
+ scrollThread.setEvent(evt);
+ }
+
+ }
+
+ // this class allows scrolling off the bottom of the visible alignment
+ class ScrollThread
+ extends Thread
+ {
+ MouseEvent evt;
+ boolean running = false;
+ public ScrollThread()
+ {
+ start();
+ }
+
+ public void setEvent(MouseEvent e)
+ {
+ evt = e;
+ }
+
+ public void stopScrolling()
+ {
+ running = false;
+ }
+
+ public void run()
+ {
+ running = true;
+ while (running)
+ {
+
+ if (evt != null)
+ {
+
+ if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+ {
+ running = ap.scrollUp(true);
+ }
+
+ if (mouseDragging && evt.getY() >= getSize().height &&
+ av.alignment.getHeight() > av.getEndSeq())
+ {
+ running = ap.scrollUp(false);
+ }
+
+ if (mouseDragging && evt.getX() < 0)
+ {
+ running = ap.scrollRight(false);
+ }
+
+ else if (mouseDragging && evt.getX() >= getSize().width)
+ {
+ running = ap.scrollRight(true);
+ }
+ }
+
+ try
+ {
+ Thread.sleep(75);
+ }
+ catch (Exception ex)
+ {}
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff