-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\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
- * 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
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.commands.EditCommand;\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-import java.util.Vector;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class SeqPanel extends JPanel implements MouseListener,\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
- 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
- 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
-\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
- int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());\r
- if (cwidth < 1)\r
- return 0;\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
- if (av.hasHiddenColumns)\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
-\r
- return res;\r
-\r
- }\r
-\r
- int findSeq(MouseEvent evt)\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 = 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
- 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
- while (index < seq.getSequenceFeatures().length)\r
- {\r
- SequenceFeature sf = seq.getSequenceFeatures()[index];\r
- if (sf.getBegin() <= res &&\r
- sf.getEnd() >= res)\r
- {\r
- if (av.featuresDisplayed.containsKey(sf.getType()))\r
- {\r
- allFeatures.addElement(sf);\r
- }\r
- }\r
- index++;\r
- }\r
- }\r
- return allFeatures;\r
- }\r
-\r
- void endEditing()\r
- {\r
- 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
- editingSeqs = false;\r
- groupEditing = false;\r
- keyboardNo1 = null;\r
- keyboardNo2 = null;\r
- editCommand = null;\r
- }\r
-\r
- void setCursorRow()\r
- {\r
- seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;\r
- scrollToVisible();\r
- }\r
-\r
- void setCursorColumn()\r
- {\r
- seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;\r
- scrollToVisible();\r
- }\r
-\r
- void setCursorRowAndColumn()\r
- {\r
- if(keyboardNo2==null)\r
- {\r
- keyboardNo2 = new StringBuffer();\r
- }\r
- else\r
- {\r
- seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;\r
- seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;\r
- scrollToVisible();\r
- }\r
- }\r
-\r
- void setCursorPosition()\r
- {\r
- SequenceI sequence =\r
- (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
-\r
- seqCanvas.cursorX = sequence.findIndex(\r
- getKeyboardNo(keyboardNo1)-1\r
- );\r
- scrollToVisible();\r
- }\r
-\r
- void moveCursor(int dx, int dy)\r
- {\r
- seqCanvas.cursorX += dx;\r
- seqCanvas.cursorY += dy;\r
- scrollToVisible();\r
- }\r
-\r
- void scrollToVisible()\r
- {\r
- if (seqCanvas.cursorX < 0)\r
- seqCanvas.cursorX = 0;\r
- else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)\r
- seqCanvas.cursorX = av.alignment.getWidth() - 1;\r
-\r
- if (seqCanvas.cursorY < 0)\r
- seqCanvas.cursorY = 0;\r
- else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)\r
- seqCanvas.cursorY = av.alignment.getHeight() - 1;\r
-\r
-\r
- endEditing();\r
- if(av.wrapAlignment)\r
- {\r
- ap.scrollToWrappedVisible(seqCanvas.cursorX);\r
- }\r
- else\r
- {\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.startRes)\r
- {\r
- if (!ap.scrollRight(false))\r
- break;\r
- }\r
- while (seqCanvas.cursorX > av.endRes)\r
- {\r
- if (!ap.scrollRight(true))\r
- break;\r
- }\r
- }\r
- }\r
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),\r
- seqCanvas.cursorX, seqCanvas.cursorY);\r
-\r
- seqCanvas.repaint();\r
- }\r
-\r
- void setSelectionAreaAtCursor(boolean topLeft)\r
- {\r
- SequenceI sequence =\r
- (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
-\r
- if(av.getSelectionGroup()!=null)\r
- {\r
- SequenceGroup sg = av.selectionGroup;\r
- //Find the top and bottom of this group\r
- int min = av.alignment.getHeight(), max = 0;\r
- for(int i=0; i<sg.getSize(false); i++)\r
- {\r
- int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
- if(index > max)\r
- max = index;\r
- if(index < min)\r
- min = index;\r
- }\r
-\r
- max ++;\r
-\r
- if(topLeft)\r
- {\r
- sg.setStartRes(seqCanvas.cursorX);\r
- if(sg.getEndRes()<seqCanvas.cursorX)\r
- sg.setEndRes(seqCanvas.cursorX);\r
-\r
- min = seqCanvas.cursorY;\r
- }\r
- else\r
- {\r
- sg.setEndRes(seqCanvas.cursorX);\r
- if(sg.getStartRes()>seqCanvas.cursorX)\r
- sg.setStartRes(seqCanvas.cursorX);\r
-\r
- max = seqCanvas.cursorY+1;\r
- }\r
-\r
- if(min>max)\r
- {\r
- // Only the user can do this\r
- av.setSelectionGroup(null);\r
- }\r
- else\r
- {\r
- // Now add any sequences between min and max\r
- sg.getSequences(false).clear();\r
- for (int i = min; i < max; i++)\r
- {\r
- sg.addSequence(av.alignment.getSequenceAt(i), false);\r
- }\r
- }\r
- }\r
-\r
- if (av.getSelectionGroup() == null)\r
- {\r
- SequenceGroup sg = new SequenceGroup();\r
- sg.setStartRes(seqCanvas.cursorX);\r
- sg.setEndRes(seqCanvas.cursorX);\r
- sg.addSequence(sequence, false);\r
- av.setSelectionGroup(sg);\r
- }\r
-\r
-\r
- ap.repaint();\r
- }\r
-\r
- void insertGapAtCursor(boolean group)\r
- {\r
- groupEditing = group;\r
- startseq = seqCanvas.cursorY;\r
- lastres = seqCanvas.cursorX;\r
- editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));\r
- endEditing();\r
- }\r
-\r
- void deleteGapAtCursor(boolean group)\r
- {\r
- groupEditing = group;\r
- startseq = seqCanvas.cursorY;\r
- lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);\r
- editSequence(false, seqCanvas.cursorX);\r
- endEditing();\r
- }\r
-\r
- void numberPressed(char value)\r
- {\r
- if(keyboardNo1==null)\r
- keyboardNo1 = new StringBuffer();\r
-\r
- if(keyboardNo2!=null)\r
- keyboardNo2.append(value);\r
- else\r
- keyboardNo1.append(value);\r
- }\r
-\r
- int getKeyboardNo(StringBuffer kb)\r
- {\r
- if(kb==null)\r
- return 1;\r
- else\r
- return Integer.parseInt(kb.toString());\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- mouseDragging = false;\r
- mouseWheelPressed = false;\r
-\r
- if (!editingSeqs)\r
- {\r
- doMouseReleasedDefineMode(evt);\r
- return;\r
- }\r
-\r
- endEditing();\r
-\r
- ap.repaint();\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\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
- if (evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
- {\r
- if (evt.isAltDown() || evt.isControlDown())\r
- {\r
- groupEditing = true;\r
- }\r
- editingSeqs = true;\r
- }\r
- else\r
- {\r
- doMousePressedDefineMode(evt);\r
- return;\r
- }\r
-\r
- int seq = findSeq(evt);\r
- int res = findRes(evt);\r
-\r
- if(seq<0 || res<0)\r
- return;\r
-\r
- if ((seq < av.getAlignment().getHeight()) &&\r
- (res < av.getAlignment().getSequenceAt(seq).getLength()))\r
- {\r
- startseq = seq;\r
- lastres = res;\r
- }\r
- else\r
- {\r
- startseq = -1;\r
- lastres = -1;\r
- }\r
-\r
- return;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- if (editingSeqs)\r
- {\r
- // This is because MacOSX creates a mouseMoved\r
- // If control is down, other platforms will not.\r
- mouseDragged(evt);\r
- }\r
-\r
- int res = findRes(evt);\r
- int seq = findSeq(evt);\r
-\r
-\r
- if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())\r
- return;\r
-\r
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
-\r
- if (res > sequence.getLength())\r
- {\r
- return;\r
- }\r
-\r
- if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
- {\r
- seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
- }\r
-\r
- setStatusMessage(sequence, res, seq);\r
-\r
- // use aa to see if the mouse pointer is on a\r
- if (av.showSequenceFeatures)\r
- {\r
- tooltipText.setLength(6); // Cuts the buffer back to <html>\r
-\r
- SequenceFeature[] features = findFeaturesAtRes(\r
- sequence.getDatasetSequence(), sequence.findPosition(res));\r
-\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
- if (features[i].getBegin() == sequence.findPosition(res)\r
- || features[i].getEnd() == sequence.findPosition(res))\r
- {\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].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
- tmpString = tmpString.substring(startTag + 6);\r
- }\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
- tmpString = tmpString.substring(0, endTag);\r
- }\r
-\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
- tooltipText.append("; ");\r
- tooltipText.append(tmpString);\r
-\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
- if (features[i].links != null)\r
- tooltipText.append(" <img src=\"" + linkImageURL + "\">");\r
-\r
- }\r
-\r
- // else if(features[i].begin==0 && features[i].end==0)\r
- {\r
- // seqSpecific.append(features[i].featureGroup+": "\r
- // + features[i].getType()+" "\r
- // +features[i].getDescription()+"<br>");\r
-\r
- }\r
- }\r
-\r
- if(tooltipText.length()==6) // <html></html>\r
- {\r
-\r
- setToolTipText("");\r
- }\r
- else\r
- {\r
- tooltipText.append("</html>");\r
- setToolTipText(tooltipText.toString());\r
- }\r
- }\r
- else\r
- setToolTipText("");\r
- }\r
- }\r
-\r
- void setStatusMessage(SequenceI sequence, int res, int seq)\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 + " (" + sequence.findPosition(res) +\r
- ")");\r
- }\r
- }\r
- ap.alignFrame.statusBar.setText(text.toString());\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\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
- return;\r
- }\r
-\r
- int res = findRes(evt);\r
-\r
- if (res < 0)\r
- {\r
- res = 0;\r
- }\r
-\r
- if ((lastres == -1) || (lastres == res))\r
- {\r
- return;\r
- }\r
-\r
- if ( (res < av.getAlignment().getWidth()) && (res < lastres))\r
- {\r
- // dragLeft, delete gap\r
- editSequence(false, res);\r
- }\r
- else\r
- editSequence(true, res);\r
-\r
- mouseDragging = true;\r
- if(scrollThread!=null)\r
- scrollThread.setEvent(evt);\r
-\r
- }\r
-\r
- synchronized void editSequence(boolean insertGap, int startres)\r
- {\r
- int fixedLeft = -1;\r
- int fixedRight = -1;\r
- boolean fixedColumns = false;\r
- SequenceGroup sg = av.getSelectionGroup();\r
-\r
-\r
- if (!groupEditing && av.hasHiddenRows)\r
- {\r
- if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
- {\r
- groupEditing = true;\r
- }\r
- }\r
-\r
- //No group, but the sequence may represent a group\r
- if (groupEditing\r
- && sg == null\r
- && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)\r
- {\r
- groupEditing = false;\r
- }\r
-\r
- SequenceI seq = av.alignment.getSequenceAt(startseq);\r
- StringBuffer message = new StringBuffer();\r
- if (groupEditing)\r
- {\r
- message.append("Edit group:");\r
- if (editCommand == null)\r
- editCommand = new EditCommand("Edit Group");\r
- }\r
- else\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
- else\r
- message.append(" delete ");\r
-\r
- message.append(Math.abs(startres-lastres)+" gaps.");\r
- ap.alignFrame.statusBar.setText(message.toString());\r
-\r
-\r
- //Are we editing within a selection group?\r
- if (groupEditing\r
- || (sg != null && sg.getSequences(true).contains(seq)))\r
- {\r
- fixedColumns = true;\r
-\r
- //sg might be null as the user may only see 1 sequence,\r
- //but the sequence represents a group\r
- if (sg == null)\r
- {\r
- sg = new SequenceGroup(null, null, false, false, false, 0,\r
- av.alignment.getWidth()-1);\r
- sg.addSequence(av.alignment.getSequenceAt(startseq), false);\r
- }\r
-\r
- fixedLeft = sg.getStartRes();\r
- fixedRight = sg.getEndRes();\r
-\r
- 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
- Vector vseqs = sg.getSequences(true);\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\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
-\r
- for (g = 0; g < groupSize; g++)\r
- {\r
- for (int j = 0; j < startres - lastres; j++)\r
- {\r
- if (!jalview.util.Comparison.isGap(\r
- groupSeqs[g].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 (g = 0; g < groupSize; g++)\r
- {\r
- for (int j = startres; j < lastres; j++)\r
- {\r
- if (groupSeqs[g].getLength() <= j)\r
- {\r
- continue;\r
- }\r
-\r
- if (!jalview.util.Comparison.isGap(\r
- groupSeqs[g].getCharAt(j)))\r
- {\r
- // Not a gap, block edit not valid\r
- endEditing();\r
- return;\r
- }\r
- }\r
- }\r
- }\r
-\r
- if (insertGap)\r
- {\r
- // dragging to the right\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- for (int j = lastres; j < startres; j++)\r
- {\r
- insertChar(j, groupSeqs, fixedRight);\r
- }\r
- }\r
- else\r
- {\r
- editCommand.appendEdit(EditCommand.INSERT_GAP,\r
- groupSeqs,\r
- startres, startres-lastres,\r
- av.getGapCharacter(),\r
- true);\r
- }\r
- }\r
- else\r
- {\r
- // dragging to the left\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- for (int j = lastres; j > startres; j--)\r
- {\r
- deleteChar(startres, groupSeqs, fixedRight);\r
- }\r
- }\r
- else\r
- editCommand.appendEdit(EditCommand.DELETE_GAP,\r
- groupSeqs,\r
- startres, lastres - startres,\r
- av.getGapCharacter(),\r
- true);\r
-\r
- }\r
- }\r
- else /////Editing a single sequence///////////\r
- {\r
- if (insertGap)\r
- {\r
- // dragging to the right\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- for (int j = lastres; j < startres; j++)\r
- {\r
- insertChar(j, new SequenceI[]{seq}, fixedRight);\r
- }\r
- }\r
- else\r
- {\r
- editCommand.appendEdit(EditCommand.INSERT_GAP,\r
- new SequenceI[]\r
- {seq},\r
- lastres, startres-lastres,\r
- av.getGapCharacter(),\r
- true);\r
- }\r
- }\r
- else\r
- {\r
- // dragging to the left\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- for (int j = lastres; j > startres; j--)\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))\r
- {\r
- endEditing();\r
- break;\r
- }\r
- deleteChar(startres, new SequenceI[]{seq}, fixedRight);\r
- }\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
- 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.getGapCharacter(),\r
- true);\r
- }\r
- }\r
- }\r
- }\r
-\r
- lastres = startres;\r
- seqCanvas.repaint();\r
- }\r
-\r
-\r
-\r
- void insertChar(int j, SequenceI [] seq, int fixedColumn)\r
- {\r
- int blankColumn = fixedColumn;\r
- for(int s=0; s<seq.length; s++)\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
-\r
- for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
- {\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
- if (blankColumn <= j)\r
- {\r
- blankColumn = fixedColumn;\r
- endEditing();\r
- return;\r
- }\r
- }\r
-\r
- editCommand.appendEdit(EditCommand.DELETE_GAP,\r
- seq,\r
- blankColumn, 1, av.getGapCharacter(), true);\r
-\r
- editCommand.appendEdit(EditCommand.INSERT_GAP,\r
- seq,\r
- j, 1, av.getGapCharacter(),\r
- true);\r
-\r
- }\r
-\r
- void deleteChar(int j, SequenceI [] seq, int fixedColumn)\r
- {\r
-\r
- editCommand.appendEdit(EditCommand.DELETE_GAP,\r
- seq,\r
- j, 1, av.getGapCharacter(), true);\r
-\r
- editCommand.appendEdit(EditCommand.INSERT_GAP,\r
- seq,\r
- fixedColumn, 1, av.getGapCharacter(), true);\r
- }\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
- 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==1)\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)\r
- {\r
- seqCanvas.getFeatureRenderer().amendFeatures(\r
- new SequenceI[]\r
- {sequence}, features, false);\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.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
-\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.structure.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.130 $
+ */
+public class SeqPanel extends JPanel implements MouseListener,
+ MouseMotionListener, MouseWheelListener, SequenceListener,
+ SelectionListener
+
+{
+ /** DOCUMENT ME!! */
+ public SeqCanvas seqCanvas;
+
+ /** DOCUMENT ME!! */
+ public AlignmentPanel ap;
+
+ protected int lastres;
+
+ protected int startseq;
+
+ protected AlignViewport av;
+
+ ScrollThread scrollThread = null;
+
+ boolean mouseDragging = false;
+
+ boolean editingSeqs = false;
+
+ boolean groupEditing = false;
+
+ // ////////////////////////////////////////
+ // ///Everything below this is for defining the boundary of the rubberband
+ // ////////////////////////////////////////
+ int oldSeq = -1;
+
+ boolean changeEndSeq = false;
+
+ boolean changeStartSeq = false;
+
+ boolean changeEndRes = false;
+
+ boolean changeStartRes = false;
+
+ SequenceGroup stretchGroup = null;
+
+ boolean remove = false;
+
+ Point lastMousePress;
+
+ boolean mouseWheelPressed = false;
+
+ StringBuffer keyboardNo1;
+
+ StringBuffer keyboardNo2;
+
+ java.net.URL linkImageURL;
+
+ StringBuffer tooltipText = new StringBuffer("<html>");
+
+ String tmpString;
+
+ EditCommand editCommand;
+
+ StructureSelectionManager ssm;
+
+ /**
+ * Creates a new SeqPanel object.
+ *
+ * @param avp
+ * DOCUMENT ME!
+ * @param p
+ * DOCUMENT ME!
+ */
+ public SeqPanel(AlignViewport av, AlignmentPanel ap)
+ {
+ linkImageURL = getClass().getResource("/images/link.gif");
+ ToolTipManager.sharedInstance().registerComponent(this);
+ ToolTipManager.sharedInstance().setInitialDelay(0);
+ ToolTipManager.sharedInstance().setDismissDelay(10000);
+ this.av = av;
+ setBackground(Color.white);
+
+ seqCanvas = new SeqCanvas(ap);
+ setLayout(new BorderLayout());
+ add(seqCanvas, BorderLayout.CENTER);
+
+ this.ap = ap;
+
+ if (!av.isDataset())
+ {
+ addMouseMotionListener(this);
+ addMouseListener(this);
+ addMouseWheelListener(this);
+ ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+ ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
+ }
+ }
+
+ 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(this.getWidth());
+ if (cwidth < 1)
+ {
+ return 0;
+ }
+
+ wrappedBlock = y / cHeight;
+ wrappedBlock += av.getStartRes() / cwidth;
+
+ res = wrappedBlock * cwidth + x / av.getCharWidth();
+
+ }
+ else
+ {
+ if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
+ {
+ // make sure we calculate relative to visible alignment, rather than right-hand gutter
+ x = seqCanvas.getX()+seqCanvas.getWidth();
+ }
+ 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);
+ }
+ else
+ {
+ seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
+ av.alignment.getHeight() - 1);
+ }
+
+ return seq;
+ }
+
+ SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+ {
+ Vector tmp = new Vector();
+ SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features != null)
+ {
+ for (int i = 0; i < features.length; i++)
+ {
+ if (av.featuresDisplayed == null
+ || !av.featuresDisplayed.containsKey(features[i].getType()))
+ {
+ continue;
+ }
+
+ if (features[i].featureGroup != null
+ && seqCanvas.fr.featureGroups != null
+ && seqCanvas.fr.featureGroups
+ .containsKey(features[i].featureGroup)
+ && !((Boolean) seqCanvas.fr.featureGroups
+ .get(features[i].featureGroup)).booleanValue())
+ continue;
+
+ if ((features[i].getBegin() <= res)
+ && (features[i].getEnd() >= res))
+ {
+ tmp.addElement(features[i]);
+ }
+ }
+ }
+
+ features = new SequenceFeature[tmp.size()];
+ tmp.copyInto(features);
+
+ return features;
+ }
+
+ void endEditing()
+ {
+ if (editCommand != null && editCommand.getSize() > 0)
+ {
+ ap.alignFrame.addHistoryItem(editCommand);
+ av.firePropertyChange("alignment", null, av.getAlignment()
+ .getSequences());
+ }
+
+ startseq = -1;
+ lastres = -1;
+ editingSeqs = false;
+ groupEditing = false;
+ keyboardNo1 = null;
+ keyboardNo2 = null;
+ editCommand = null;
+ }
+
+ void setCursorRow()
+ {
+ seqCanvas.cursorY = getKeyboardNo1() - 1;
+ scrollToVisible();
+ }
+
+ void setCursorColumn()
+ {
+ seqCanvas.cursorX = getKeyboardNo1() - 1;
+ scrollToVisible();
+ }
+
+ void setCursorRowAndColumn()
+ {
+ if (keyboardNo2 == null)
+ {
+ keyboardNo2 = new StringBuffer();
+ }
+ else
+ {
+ seqCanvas.cursorX = getKeyboardNo1() - 1;
+ seqCanvas.cursorY = getKeyboardNo2() - 1;
+ scrollToVisible();
+ }
+ }
+
+ void setCursorPosition()
+ {
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ seqCanvas.cursorY);
+
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+ scrollToVisible();
+ }
+
+ void moveCursor(int dx, int dy)
+ {
+ seqCanvas.cursorX += dx;
+ seqCanvas.cursorY += dy;
+ if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+ {
+ int original = seqCanvas.cursorX - dx;
+ int maxWidth = av.alignment.getWidth();
+
+ while (!av.colSel.isVisible(seqCanvas.cursorX)
+ && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+ {
+ seqCanvas.cursorX += dx;
+ }
+
+ if (seqCanvas.cursorX >= maxWidth
+ || !av.colSel.isVisible(seqCanvas.cursorX))
+ {
+ seqCanvas.cursorX = original;
+ }
+ }
+
+ 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);
+ }
+ if (!av.wrapAlignment)
+ {
+ while (seqCanvas.cursorX < av.colSel
+ .adjustForHiddenColumns(av.startRes))
+ {
+ if (!ap.scrollRight(false))
+ {
+ break;
+ }
+ }
+ while (seqCanvas.cursorX > av.colSel
+ .adjustForHiddenColumns(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(); 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(null).clear();
+ 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.paintAlignment(false);
+ av.sendSelection();
+ }
+
+ void insertGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
+ endEditing();
+ }
+
+ void deleteGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX + getKeyboardNo1();
+ editSequence(false, false, seqCanvas.cursorX);
+ endEditing();
+ }
+
+ void insertNucAtCursor(boolean group,String nuc){
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
+ endEditing();
+ }
+
+ void numberPressed(char value)
+ {
+ if (keyboardNo1 == null)
+ {
+ keyboardNo1 = new StringBuffer();
+ }
+
+ if (keyboardNo2 != null)
+ {
+ keyboardNo2.append(value);
+ }
+ else
+ {
+ keyboardNo1.append(value);
+ }
+ }
+
+ int getKeyboardNo1()
+ {
+ if (keyboardNo1 == null)
+ return 1;
+ else
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
+ }
+
+ int getKeyboardNo2()
+ {
+ if (keyboardNo2 == null)
+ return 1;
+ else
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent evt)
+ {
+ mouseDragging = false;
+ mouseWheelPressed = false;
+
+ if (!editingSeqs)
+ {
+ doMouseReleasedDefineMode(evt);
+ return;
+ }
+
+ endEditing();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mousePressed(MouseEvent evt)
+ {
+ lastMousePress = evt.getPoint();
+
+ if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+ {
+ mouseWheelPressed = true;
+ return;
+ }
+
+ if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
+ {
+ if (evt.isAltDown() || evt.isControlDown())
+ {
+ groupEditing = true;
+ }
+ editingSeqs = true;
+ }
+ else
+ {
+ doMousePressedDefineMode(evt);
+ return;
+ }
+
+ int seq = findSeq(evt);
+ int res = findRes(evt);
+
+ if (seq < 0 || res < 0)
+ {
+ return;
+ }
+
+ if ((seq < av.getAlignment().getHeight())
+ && (res < av.getAlignment().getSequenceAt(seq).getLength()))
+ {
+ startseq = seq;
+ lastres = res;
+ }
+ else
+ {
+ startseq = -1;
+ lastres = -1;
+ }
+
+ return;
+ }
+
+ String lastMessage;
+
+ public void mouseOverSequence(SequenceI sequence, int index, int pos)
+ {
+ String tmp = sequence.hashCode() + " " + index + " " + pos;
+
+ if (lastMessage == null || !lastMessage.equals(tmp))
+ {
+ // System.err.println("mouseOver Sequence: "+tmp);
+ ssm.mouseOverSequence(sequence, index, pos, av);
+ }
+ lastMessage = tmp;
+ }
+
+ public void highlightSequence(SearchResults results)
+ {
+ if (av.followHighlight)
+ {
+ if (ap.scrollToPosition(results, false))
+ {
+ seqCanvas.revalidate();
+ }
+ }
+ seqCanvas.highlightSearchResults(results);
+ }
+
+ public void updateColours(SequenceI seq, int index)
+ {
+ System.out.println("update the seqPanel colours");
+ // repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent evt)
+ {
+ if (editingSeqs)
+ {
+ // This is because MacOSX creates a mouseMoved
+ // If control is down, other platforms will not.
+ mouseDragged(evt);
+ }
+
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+ int pos;
+ if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+ {
+ return;
+ }
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+ if (res >= sequence.getLength())
+ {
+ return;
+ }
+
+ pos = setStatusMessage(sequence, res, seq);
+ if (ssm != null && pos > -1)
+ mouseOverSequence(sequence, res, pos);
+
+ tooltipText.setLength(6); // Cuts the buffer back to <html>
+
+ SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ if (groups != null)
+ {
+ for (int g = 0; g < groups.length; g++)
+ {
+ if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+ {
+ if (tooltipText.length() > 6)
+ {
+ tooltipText.append("<br>");
+ }
+
+ if (!groups[g].getName().startsWith("JTreeGroup")
+ && !groups[g].getName().startsWith("JGroup"))
+ {
+ tooltipText.append(groups[g].getName());
+ }
+
+ if (groups[g].getDescription() != null)
+ {
+ tooltipText.append(": " + groups[g].getDescription());
+ }
+ }
+ }
+ }
+
+ // use aa to see if the mouse pointer is on a
+ if (av.showSequenceFeatures)
+ {
+ int rpos;
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence.getDatasetSequence(),
+ rpos = sequence.findPosition(res));
+ appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
+ this.ap.seqPanel.seqCanvas.fr.minmax);
+ }
+ if (tooltipText.length() == 6) // <html></html>
+ {
+ setToolTipText(null);
+ lastTooltip = null;
+ }
+ else
+ {
+ tooltipText.append("</html>");
+ if (lastTooltip == null
+ || !lastTooltip.equals(tooltipText.toString()))
+ {
+ setToolTipText(tooltipText.toString());
+ lastTooltip = tooltipText.toString();
+ }
+
+ }
+
+ }
+
+ private Point lastp = null;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
+ */
+ public Point getToolTipLocation(MouseEvent event)
+ {
+ int x = event.getX(), w = getWidth();
+ int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
+ // close to edge
+ Point p = lastp;
+ if (!event.isShiftDown() || p == null)
+ {
+ p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
+ event.getX() + wdth, event.getY() - 20) : null;
+ }
+ /*
+ * TODO: try to modify position region is not obcured by tooltip
+ */
+ return lastp = p;
+ }
+
+ /**
+ * appends the features at rpos to the given stringbuffer ready for display in
+ * a tooltip
+ *
+ * @param tooltipText2
+ * @param linkImageURL
+ * @param rpos
+ * @param features
+ * TODO refactor to Jalview 'utilities' somehow.
+ */
+ public void appendFeatures(StringBuffer tooltipText2,
+ String linkImageURL, int rpos, SequenceFeature[] features)
+ {
+ appendFeatures(tooltipText2, linkImageURL, rpos, features, null);
+ }
+
+ public void appendFeatures(StringBuffer tooltipText2, String string,
+ int rpos, SequenceFeature[] features, Hashtable minmax)
+ {
+ String tmpString;
+ if (features != null)
+ {
+ for (int i = 0; i < features.length; i++)
+ {
+ if (features[i].getType().equals("disulfide bond"))
+ {
+ if (features[i].getBegin() == rpos
+ || features[i].getEnd() == rpos)
+ {
+ if (tooltipText2.length() > 6)
+ {
+ tooltipText2.append("<br>");
+ }
+ tooltipText2.append("disulfide bond " + features[i].getBegin()
+ + ":" + features[i].getEnd());
+ if (features[i].links != null)
+ {
+ tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
+ }
+ }
+ }
+ else
+ {
+ if (tooltipText2.length() > 6)
+ {
+ tooltipText2.append("<br>");
+ }
+ // TODO: remove this hack to display link only features
+ boolean linkOnly = features[i].getValue("linkonly") != null;
+ if (!linkOnly)
+ {
+ tooltipText2.append(features[i].getType() + " ");
+ if (rpos != 0)
+ {
+ // we are marking a positional feature
+ tooltipText2.append(features[i].begin);
+ }
+ if (features[i].begin != features[i].end)
+ {
+ tooltipText2.append(" " + features[i].end);
+ }
+
+ if (features[i].getDescription() != null
+ && !features[i].description.equals(features[i]
+ .getType()))
+ {
+ tmpString = features[i].getDescription();
+ String tmp2up=tmpString.toUpperCase();
+ int startTag = tmp2up.indexOf("<HTML>");
+ if (startTag > -1)
+ {
+ tmpString = tmpString.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag+6);
+ }
+ int endTag = tmp2up.indexOf("</BODY>");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
+ }
+ endTag = tmp2up.indexOf("</HTML>");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ }
+
+ if (startTag > -1)
+ {
+ tooltipText2.append("; " + tmpString);
+ }
+ else
+ {
+ if (tmpString.indexOf("<") > -1
+ || tmpString.indexOf(">") > -1)
+ {
+ // The description does not specify html is to
+ // be used, so we must remove < > symbols
+ tmpString = tmpString.replaceAll("<", "<");
+ tmpString = tmpString.replaceAll(">", ">");
+
+ tooltipText2.append("; ");
+ tooltipText2.append(tmpString);
+
+ }
+ else
+ {
+ tooltipText2.append("; " + tmpString);
+ }
+ }
+ }
+ // check score should be shown
+ if (features[i].getScore() != Float.NaN)
+ {
+ float[][] rng = (minmax == null) ? null : ((float[][]) minmax
+ .get(features[i].getType()));
+ if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
+ {
+ tooltipText2.append(" Score=" + features[i].getScore());
+ }
+ }
+ if (features[i].getValue("status") != null)
+ {
+ String status = features[i].getValue("status").toString();
+ if (status.length() > 0)
+ {
+ tooltipText2.append("; (" + features[i].getValue("status")
+ + ")");
+ }
+ }
+ }
+ if (features[i].links != null)
+ {
+ tooltipText2.append(" <img src=\"" + linkImageURL + "\">");
+ }
+
+ }
+ }
+ }
+ }
+
+ String lastTooltip;
+
+ /**
+ * Set status message in alignment panel
+ *
+ * @param sequence
+ * aligned sequence object
+ * @param res
+ * alignment column
+ * @param seq
+ * index of sequence in alignment
+ * @return position of res in sequence
+ */
+ int setStatusMessage(SequenceI sequence, int res, int seq)
+ {
+ int pos = -1;
+ 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)
+ {
+ pos = sequence.findPosition(res);
+ if (obj != "")
+ {
+ text.append(obj + " (" + pos + ")");
+ }
+ }
+ ap.alignFrame.statusBar.setText(text.toString());
+ return pos;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ 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.getY()) > Math.abs(evt
+ .getX() - lastMousePress.getX()))
+ {
+ int fontSize = av.font.getSize();
+
+ if (evt.getY() < lastMousePress.getY())
+ {
+ fontSize--;
+ }
+ else if (evt.getY() > lastMousePress.getY())
+ {
+ fontSize++;
+ }
+
+ if (fontSize < 1)
+ {
+ fontSize = 1;
+ }
+
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+ av.charWidth = oldWidth;
+ ap.fontChanged();
+ }
+ else
+ {
+ if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+ {
+ av.charWidth--;
+ }
+ else if (evt.getX() > lastMousePress.getX())
+ {
+ av.charWidth++;
+ }
+
+ ap.paintAlignment(false);
+ }
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+ lastMousePress = evt.getPoint();
+
+ 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, false,res);
+ }
+ else
+ {
+ editSequence(true, false,res);
+ }
+
+ mouseDragging = true;
+ if (scrollThread != null)
+ {
+ scrollThread.setEvent(evt);
+ }
+ }
+
+ //TODO: Make it more clever than many booleans
+ synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
+ {
+ int fixedLeft = -1;
+ int fixedRight = -1;
+ boolean fixedColumns = false;
+ SequenceGroup sg = av.getSelectionGroup();
+
+ SequenceI seq = av.alignment.getSequenceAt(startseq);
+
+ // No group, but the sequence may represent a group
+ if (!groupEditing && av.hasHiddenRows)
+ {
+ if (av.hiddenRepSequences != null
+ && av.hiddenRepSequences.containsKey(seq))
+ {
+ sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ groupEditing = true;
+ }
+ }
+
+ StringBuffer message = new StringBuffer();
+ if (groupEditing)
+ {
+ message.append("Edit group:");
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand("Edit Group");
+ }
+ }
+ else
+ {
+ message.append("Edit sequence: " + seq.getName());
+ String label = seq.getName();
+ if (label.length() > 10)
+ {
+ label = label.substring(0, 10);
+ }
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand("Edit " + label);
+ }
+ }
+
+ 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(av.hiddenRepSequences)
+ .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)
+ {
+ if (av.hiddenRepSequences == null
+ || !av.hiddenRepSequences.containsKey(seq))
+ {
+ endEditing();
+ return;
+ }
+ sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ }
+
+ 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)
+ {
+ Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+ int g, groupSize = vseqs.size();
+ SequenceI[] groupSeqs = new SequenceI[groupSize];
+ for (g = 0; g < groupSeqs.length; g++)
+ {
+ groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+ }
+
+ // 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 (g = 0; g < groupSize; g++)
+ {
+ for (int j = 0; j < startres - lastres; j++)
+ {
+ if (!jalview.util.Comparison.isGap(groupSeqs[g]
+ .getCharAt(fixedRight - j)))
+ {
+ blank = false;
+ break;
+ }
+ }
+ }
+ if (blank)
+ {
+ break;
+ }
+ }
+
+ if (!blank)
+ {
+ if (sg.getSize() == 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 (g = 0; g < groupSize; g++)
+ {
+ for (int j = startres; j < lastres; j++)
+ {
+ if (groupSeqs[g].getLength() <= j)
+ {
+ continue;
+ }
+
+ if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+ {
+ // Not a gap, block edit not valid
+ endEditing();
+ return;
+ }
+ }
+ }
+ }
+
+ if (insertGap)
+ {
+ // dragging to the right
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, groupSeqs, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+ startres, startres - lastres, av.alignment, true);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j > startres; j--)
+ {
+ deleteChar(startres, groupSeqs, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+ startres, lastres - startres, av.alignment, true);
+ }
+
+ }
+ }
+ else
+ // ///Editing a single sequence///////////
+ {
+ if (insertGap)
+ {
+ // dragging to the right
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, new SequenceI[]
+ { seq }, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+ { seq }, lastres, startres - lastres, av.alignment, true);
+ }
+ }
+ else
+ {
+ if(!editSeq){
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j > startres; j--)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+ {
+ endEditing();
+ break;
+ }
+ deleteChar(startres, new SequenceI[]
+ { seq }, fixedRight);
+ }
+ }
+ else
+ {
+ // could be a keyboard edit trying to delete none gaps
+ int max = 0;
+ for (int m = startres; m < lastres; m++)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ {
+ break;
+ }
+ max++;
+ }
+
+ if (max > 0)
+ {
+ editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+ { seq }, startres, max, av.alignment, true);
+ }
+ }
+ }else{//insertGap==false AND editSeq==TRUE;
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, new SequenceI[]
+ { seq }, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
+ { seq }, lastres, startres - lastres, av.alignment, true);
+ }
+ }
+ }
+ }
+
+ lastres = startres;
+ seqCanvas.repaint();
+ }
+
+ void insertChar(int j, SequenceI[] seq, int fixedColumn)
+ {
+ int blankColumn = fixedColumn;
+ for (int s = 0; s < seq.length; s++)
+ {
+ // Find the next gap before the end of the visible region boundary
+ // If lastCol > j, theres a boundary after the gap insertion
+
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+ {
+ if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+ {
+ // Theres a space, so break and insert the gap
+ break;
+ }
+ }
+
+ if (blankColumn <= j)
+ {
+ blankColumn = fixedColumn;
+ endEditing();
+ return;
+ }
+ }
+
+ editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+ av.alignment, true);
+
+ editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
+ true);
+
+ }
+
+ void deleteChar(int j, SequenceI[] seq, int fixedColumn)
+ {
+
+ editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
+ true);
+
+ editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+ av.alignment, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent e)
+ {
+ if (oldSeq < 0)
+ {
+ oldSeq = 0;
+ }
+
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging)
+ {
+ scrollThread = new ScrollThread();
+ }
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ SequenceGroup sg = null;
+ SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ if (evt.getClickCount() > 1)
+ {
+ sg = av.getSelectionGroup();
+ if (sg != null && sg.getSize() == 1
+ && sg.getEndRes() - sg.getStartRes() < 2)
+ {
+ av.setSelectionGroup(null);
+ }
+
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence.getDatasetSequence(),
+ sequence.findPosition(findRes(evt)));
+
+ if (features != null && features.length > 0)
+ {
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequence, features[0].getBegin(),
+ features[0].getEnd());
+ seqCanvas.highlightSearchResults(highlight);
+ }
+ if (features != null && features.length > 0)
+ {
+ seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
+ { sequence }, features, false, ap);
+
+ seqCanvas.highlightSearchResults(null);
+ }
+ }
+ }
+
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ e.consume();
+ if (e.getWheelRotation() > 0)
+ {
+ ap.scrollUp(false);
+ }
+ else
+ {
+ ap.scrollUp(true);
+ }
+ // TODO Update tooltip for new position.
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void doMousePressedDefineMode(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+ oldSeq = seq;
+
+ startWrapBlock = wrappedBlock;
+
+ if (av.wrapAlignment && seq > av.alignment.getHeight())
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Cannot edit annotations in wrapped view.",
+ "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ if (seq < 0 || res < 0)
+ {
+ 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(null).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);
+
+ }
+
+ if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ {
+ SequenceFeature[] allFeatures = findFeaturesAtRes(
+ sequence.getDatasetSequence(), sequence.findPosition(res));
+ Vector links = new Vector();
+ for (int i = 0; i < allFeatures.length; i++)
+ {
+ if (allFeatures[i].links != null)
+ {
+ for (int j = 0; j < allFeatures[i].links.size(); j++)
+ {
+ links.addElement(allFeatures[i].links.elementAt(j));
+ }
+ }
+ }
+
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+ pop.show(this, evt.getX(), evt.getY());
+ return;
+ }
+
+ if (av.cursorMode)
+ {
+ seqCanvas.cursorX = findRes(evt);
+ seqCanvas.cursorY = findSeq(evt);
+ seqCanvas.repaint();
+ return;
+ }
+
+ if (stretchGroup == null)
+ {
+ // Only if left mouse button do we want to change group sizes
+
+ // 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");
+ }
+ if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if ((stretchGroup != null)
+ && (stretchGroup.getStartRes() == res))
+ {
+ // Edit end res position of selected group
+ changeStartRes = true;
+ }
+ stretchGroup.getWidth();
+ }
+
+ seqCanvas.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void doMouseReleasedDefineMode(MouseEvent evt)
+ {
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ stretchGroup.recalcConservation(); // always do this - annotation has own
+ // state
+ if (stretchGroup.cs != null)
+ {
+ if (stretchGroup.cs instanceof ClustalxColourScheme)
+ {
+ ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+ stretchGroup.getSequences(av.hiddenRepSequences),
+ stretchGroup.getWidth());
+ }
+
+ if (stretchGroup.cs.conservationApplied())
+ {
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ }
+ else
+ {
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ }
+ }
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ ap.paintAlignment(true);
+
+ changeEndRes = false;
+ changeStartRes = false;
+ stretchGroup = null;
+ av.sendSelection();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void doMouseDraggedDefineMode(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int y = findSeq(evt);
+
+ if (wrappedBlock != startWrapBlock)
+ {
+ return;
+ }
+
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ 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 < av.getStartRes())
+ {
+ res = av.getStartRes();
+ }
+
+ 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(null).contains(nextSeq))
+ {
+ stretchGroup.deleteSequence(seq, false);
+ }
+ else
+ {
+ if (seq != null)
+ {
+ stretchGroup.addSequence(seq, false);
+ }
+
+ stretchGroup.addSequence(nextSeq, false);
+ }
+ }
+
+ if (oldSeq < 0)
+ {
+ oldSeq = -1;
+ }
+
+ mouseDragging = true;
+
+ if (scrollThread != null)
+ {
+ scrollThread.setEvent(evt);
+ }
+
+ seqCanvas.repaint();
+ }
+
+ 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() >= getHeight())
+ && (av.alignment.getHeight() > av.getEndSeq()))
+ {
+ running = ap.scrollUp(false);
+ }
+
+ if (mouseDragging && (evt.getX() < 0))
+ {
+ running = ap.scrollRight(false);
+ }
+ else if (mouseDragging && (evt.getX() >= getWidth()))
+ {
+ running = ap.scrollRight(true);
+ }
+ }
+
+ try
+ {
+ Thread.sleep(20);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
+
+ /**
+ * modify current selection according to a received message.
+ */
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ SelectionSource source)
+ {
+ // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+ // handles selection messages...
+ // TODO: extend config options to allow user to control if selections may be
+ // shared between viewports.
+ if (av == source
+ || !av.followSelection
+ || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+ || (source instanceof AlignViewport && ((AlignViewport) source)
+ .getSequenceSetId().equals(av.getSequenceSetId())))
+ {
+ return;
+ }
+ // do we want to thread this ? (contention with seqsel and colsel locks, I
+ // suspect)
+ // rules are: colsel is copied if there is a real intersection between
+ // sequence selection
+ boolean repaint = false, copycolsel = true;
+ // if (!av.isSelectionGroupChanged(false))
+ {
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize()>0)
+ {
+ if (av.alignment == null)
+ {
+ jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
+ + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+ + " 's alignment is NULL! returning immediatly.");
+ return;
+ }
+ sgroup = seqsel.intersect(av.alignment,
+ (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+ if ((sgroup == null || sgroup.getSize() == 0)
+ || (colsel == null || colsel.size() == 0))
+ {
+ // don't copy columns if the region didn't intersect.
+ copycolsel = false;
+ }
+ }
+ if (sgroup != null && sgroup.getSize() > 0)
+ {
+ av.setSelectionGroup(sgroup);
+ }
+ else
+ {
+ av.setSelectionGroup(null);
+ }
+ av.isSelectionGroupChanged(true);
+ repaint = true;
+ }
+ if (copycolsel)
+ {
+ // the current selection is unset or from a previous message
+ // so import the new colsel.
+ if (colsel == null || colsel.size() == 0)
+ {
+ if (av.colSel != null)
+ {
+ av.colSel.clear();
+ repaint=true;
+ }
+ }
+ else
+ {
+ // TODO: shift colSel according to the intersecting sequences
+ if (av.colSel == null)
+ {
+ av.colSel = new ColumnSelection(colsel);
+ }
+ else
+ {
+ av.colSel.setElementsFrom(colsel);
+ }
+ }
+ av.isColSelChanged(true);
+ repaint = true;
+ }
+ if (copycolsel && av.hasHiddenColumns
+ && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+ {
+ System.err.println("Bad things");
+ }
+ if (repaint)
+ {
+ // probably finessing with multiple redraws here
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // ap.paintAlignment(false);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff