+/*\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
package jalview.gui;\r
\r
+import jalview.datamodel.*;\r
+\r
+import jalview.schemes.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import jalview.datamodel.*;\r
+\r
import javax.swing.*;\r
-import jalview.schemes.*;\r
\r
\r
-public class SeqPanel extends JPanel\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
+ // if character is inserted or deleted, we will need to recalculate the conservation\r
+ boolean seqEditOccurred = false;\r
+ ScrollThread scrollThread = null;\r
+ boolean mouseDragging = false;\r
+ boolean editingSeqs = false;\r
+ boolean groupEditing = false;\r
+\r
+ //////////////////////////////////////////\r
+ /////Everything below this is for defining the boundary of the rubberband\r
+ //////////////////////////////////////////\r
+ int oldSeq = -1;\r
+ boolean changeEndSeq = false;\r
+ boolean changeStartSeq = false;\r
+ boolean changeEndRes = false;\r
+ boolean changeStartRes = false;\r
+ SequenceGroup stretchGroup = null;\r
+ boolean remove = false;\r
+\r
+ boolean mouseWheelPressed = false;\r
+\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
+ 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
+\r
+ int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());\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
+\r
+ int seq = 0;\r
+ int y = evt.getY();\r
\r
- public AlignmentI align;\r
- public SeqCanvas seqCanvas;\r
- public AlignmentPanel parent;\r
+ if (av.wrapAlignment)\r
+ {\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- protected int startres;\r
- protected int lastres;\r
- protected int endres;\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap + seqCanvas.getAnnotationHeight();\r
\r
- protected int startseq;\r
- protected int padseq;\r
+ y -= hgap;\r
\r
- public boolean editFlag;\r
- protected AlignViewport av;\r
+ seq = ( (y % cHeight) / av.getCharHeight());\r
+ }\r
+ else\r
+ {\r
+ seq = (y / av.getCharHeight()) + av.getStartSeq();\r
+ }\r
\r
- public SeqPanel(AlignViewport av, AlignmentPanel p) {\r
- this.av = av;\r
- this.align = av.getAlignment();\r
+ return seq;\r
+ }\r
+\r
+ void endEditing()\r
+ {\r
+ startseq = -1;\r
+ lastres = -1;\r
+ seqEditOccurred = false;\r
+ editingSeqs = false;\r
+ groupEditing = false;\r
+ keyboardGaps = null;\r
+ }\r
\r
- seqCanvas = new SeqCanvas(av);\r
- setLayout(new BorderLayout());\r
- add(seqCanvas, BorderLayout.CENTER);\r
\r
- parent = p;\r
+ void moveCursor(int dx, int dy)\r
+ {\r
+ seqCanvas.cursorX += dx;\r
+ seqCanvas.cursorY += dy;\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
+ if(seqCanvas.cursorX<av.startRes)\r
+ ap.scrollRight(false);\r
+ else if(seqCanvas.cursorX>av.endRes)\r
+ ap.scrollRight(true);\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
+ if(seqCanvas.cursorY<av.startSeq)\r
+ ap.scrollUp(true);\r
+ else if(seqCanvas.cursorY+1>av.endSeq)\r
+ ap.scrollUp(false);\r
+\r
+ setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),\r
+ seqCanvas.cursorX, seqCanvas.cursorY);\r
+ seqCanvas.repaint();\r
+ }\r
\r
- addMouseMotionListener( new MouseMotionAdapter()\r
+ void setSelectionAreaAtCursor(boolean topLeft)\r
{\r
- public void mouseMoved(MouseEvent evt)\r
- { doMouseMoved(evt); }\r
- public void mouseDragged(MouseEvent evt)\r
- { doMouseDragged(evt); }\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(); 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.sequences.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
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
+ av.alignment, HistoryItem.EDIT));\r
+ groupEditing = group;\r
+ startseq = seqCanvas.cursorY;\r
+ lastres = seqCanvas.cursorX;\r
+ editSequence(true, seqCanvas.cursorX+getKeyboardGaps());\r
+ editOccurred();\r
+ }\r
+\r
+ void deleteGapAtCursor(boolean group)\r
+ {\r
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
+ av.alignment, HistoryItem.EDIT));\r
+ groupEditing = group;\r
+ startseq = seqCanvas.cursorY;\r
+ lastres = seqCanvas.cursorX+getKeyboardGaps();\r
+ editSequence(false, seqCanvas.cursorX);\r
+ editOccurred();\r
+ }\r
+\r
+ void numberPressed(char value)\r
+ {\r
+ if(keyboardGaps==null)\r
+ keyboardGaps = new StringBuffer();\r
+\r
+ keyboardGaps.append(value);\r
+ }\r
+\r
+ StringBuffer keyboardGaps;\r
+ int getKeyboardGaps()\r
+ {\r
+ if(keyboardGaps==null)\r
+ return 1;\r
+ else\r
+ return Integer.parseInt(keyboardGaps.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
- addMouseListener( new MouseAdapter()\r
+ editOccurred();\r
+\r
+ endEditing();\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
- public void mouseReleased(MouseEvent evt)\r
- { doMouseReleased(evt); }\r
- public void mousePressed(MouseEvent evt)\r
- { doMousePressed(evt); }\r
+ if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
+ {\r
+ mouseWheelPressed = true;\r
+ return;\r
+ }\r
\r
- });\r
- repaint();\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
\r
- public void doMouseReleased(MouseEvent evt) {\r
\r
- int x = evt.getX();\r
- int res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
+ int seq = findSeq(evt);\r
+ int res = findRes(evt);\r
\r
- endres = res;\r
+ if(seq<0 || res<0)\r
+ return;\r
\r
- // This is to detect edits - we're at the end of an edit if mouse is up\r
- editFlag = false;\r
- startseq = -1;\r
- startres = -1;\r
- lastres = -1;\r
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
+ av.alignment, HistoryItem.EDIT));\r
\r
- parent.RefreshPanels();\r
- repaint();\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
- }\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
- public void doMousePressed(MouseEvent evt) {\r
- int seq;\r
- int res;\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
\r
- int x = evt.getX();\r
- int y = evt.getY();\r
\r
- res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
- seq = (y)/av.getCharHeight() + av.getStartSeq();\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 (seq < align.getHeight() && res < align.getSequenceAt(seq).getLength())\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
+ SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();\r
+ if(features!=null)\r
+ {\r
+ StringBuffer sbuffer = new StringBuffer("<html>");\r
+\r
+ for (int i = 0; i < features.length; i++)\r
+ {\r
+\r
+ if ( (features[i].getBegin() <= sequence.findPosition(res)) &&\r
+ (features[i].getEnd() >= sequence.findPosition(res)))\r
+ {\r
+ if(av.featuresDisplayed==null\r
+ || !av.featuresDisplayed.containsKey(features[i].getType()))\r
+ continue;\r
+\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 (sbuffer.length() > 6)\r
+ sbuffer.append("<br>");\r
+ sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +\r
+ features[i].getEnd());\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (sbuffer.length() > 6)\r
+ sbuffer.append("<br>");\r
+ if(features[i].featureGroup!=null)\r
+ sbuffer.append(features[i].featureGroup+";");\r
+\r
+ sbuffer.append(features[i].getType());\r
+\r
+ if (features[i].getDescription() != null\r
+ && !features[i].description.equals(features[i].getType()))\r
+ sbuffer.append("; " + features[i].getDescription());\r
+\r
+ if (features[i].getStatus() != null && features[i].getStatus().length()>0)\r
+ {\r
+ sbuffer.append("; (" + features[i].getStatus() + ")");\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ sbuffer.append("</html>");\r
+ if(sbuffer.length()==13) // <html></html>\r
+ setToolTipText("");\r
+ else\r
+ setToolTipText(sbuffer.toString());\r
+ }\r
+ else\r
+ setToolTipText("");\r
+ }\r
+ }\r
+\r
+ void setStatusMessage(SequenceI sequence, int res, int seq)\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
+ 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
- startseq = seq;\r
+ }\r
\r
- if (startseq == (align.getHeight()-1)) {\r
- padseq = 1;\r
- } else {\r
- padseq = 1;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (!editingSeqs)\r
+ {\r
+ doMouseDraggedDefineMode(evt);\r
+ return;\r
}\r
\r
- startres = res;\r
- lastres = res;\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
- } else {\r
- startseq = -1;\r
- startres = -1;\r
- lastres = -1;\r
}\r
\r
- return;\r
- }\r
-\r
- public void doMouseMoved(MouseEvent evt)\r
- {\r
-\r
- int res = (int)(evt.getX()/av.getCharWidth()) + av.getStartRes();\r
- int seq = (evt.getY())/av.getCharHeight() + av.getStartSeq();\r
- if(seq>=av.getAlignment().getHeight())\r
- return;\r
-\r
- Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;\r
- String aa = "";\r
- if(obj!=null)\r
- aa = obj.toString();\r
-\r
- StringBuffer text = new StringBuffer("Sequence " +seq+" ID: "+av.getAlignment().getSequenceAt(seq).getName());\r
- if(aa!="")\r
- text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");\r
-\r
- parent.alignFrame.statusBar.setText(text.toString());\r
-\r
- }\r
-\r
- public void doMouseDragged(MouseEvent evt) {\r
- // If we're dragging we're editing\r
- editFlag = true;\r
-\r
- int x = evt.getX();\r
-\r
- int res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
- if (res < 0) {res = 0;}\r
-\r
- if (res != lastres) {\r
- if (startseq != -1) {\r
-\r
- // Group editing\r
- if (av.getGroupEdit()) {\r
- SequenceGroup sg = align.findGroup(startseq);\r
-\r
- if (res < align.getWidth() && res < lastres) {\r
- boolean flag = false;\r
- for (int i= 0 ; i < sg.getSize(); i++) {\r
- SequenceI s = (SequenceI)sg.getSequenceAt(i);\r
- for (int j=lastres-1; j >= res; j--) {\r
- if (!flag) {\r
- if (!s.getSequence().substring(j,j+1).equals(align.getGapCharacter()) &&\r
- !s.getSequence().substring(j,j+1).equals(" ")) {\r
- res = j+1;\r
- System.out.print("\07");\r
- System.out.flush();\r
- flag = true;\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- for (int i= 0 ; i < sg.getSize(); i++)\r
+ void editSequence(boolean insertGap, int startres)\r
+ {\r
+ int fixedLeft = -1;\r
+ int fixedRight = -1;\r
+ boolean fixedColumns = false;\r
+\r
+ if(insertGap && av.hasHiddenColumns)\r
+ {\r
+ //Stop editing if the user has dragged beyond hiddenBoundary\r
+ fixedRight = av.getColumnSelection().getHiddenRegionBoundary(lastres);\r
+ if( fixedRight < lastres)\r
+ {\r
+ if(lastres!=fixedRight)\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ }\r
+\r
+ if (!groupEditing && av.hasHiddenRows)\r
+ {\r
+ if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)\r
+ {\r
+ groupEditing = true;\r
+ }\r
+ }\r
+\r
+\r
+ SequenceI seq = av.alignment.getSequenceAt(startseq);\r
+ StringBuffer message = new StringBuffer();\r
+ if (groupEditing)\r
+ message.append("Edit group:");\r
+ else\r
+ message.append("Edit sequence: "+seq.getName());\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
+ || (av.getSelectionGroup() != null &&\r
+ av.getSelectionGroup().sequences.contains(seq)))\r
+ {\r
+ fixedColumns = true;\r
+\r
+ fixedLeft = av.getSelectionGroup().getStartRes();\r
+ fixedRight = av.getSelectionGroup().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
+ if (groupEditing)\r
+ {\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ if(fixedLeft>sg.getEndRes()\r
+ ||fixedRight<sg.getStartRes())\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ if (av.hasHiddenRows)\r
+ {\r
+ //sg might be null as the user may only see 1 sequence\r
+ if (sg == null)\r
+ {\r
+ sg = new SequenceGroup();\r
+ sg.addSequence(av.alignment.getSequenceAt(startseq), false);\r
+ }\r
+\r
+ SequenceGroup tmp = new SequenceGroup();\r
+\r
+ //Do any of the sequences have hidden associates?\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ seq = sg.getSequenceAt(s);\r
+ tmp.addSequence(seq, false);\r
+ if (seq.getHiddenSequences() != null)\r
+ {\r
+ for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)\r
+ tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),\r
+ false);\r
+ }\r
+ }\r
+\r
+ sg = tmp;\r
+ }\r
+\r
+ if (sg == null)\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ // int blankColumn = -1;\r
+\r
+ // drag to right\r
+ if (insertGap)\r
{\r
- SequenceI s = (SequenceI)sg.getSequenceAt(i);\r
- boolean found = false;\r
- int sno = -1;\r
- for (int k = 0; k < align.getHeight(); k++)\r
+ // Is it valid??\r
+ // Find the next gap before the end\r
+ // of the visible region boundary\r
+ if (av.hasHiddenColumns)\r
{\r
- if (align.getSequenceAt(k) == s)\r
+ // int lastCol = av.getColumnSelection().\r
+ // getHiddenRegionBoundary(res);\r
+\r
+ }\r
+\r
+ if (fixedRight != startres && fixedRight<av.alignment.getWidth()-1)\r
{\r
- found = true;\r
- sno = k;\r
- break;\r
- }\r
- }\r
- if (found && sno != -1) {\r
- if (res < align.getWidth() && res > lastres)\r
+ for (fixedRight = fixedRight;\r
+ fixedRight > lastres;\r
+ fixedRight --)\r
+ {\r
+ boolean blank = true;\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ seq = sg.getSequenceAt(s);\r
+\r
+ if (seq.getSequence().length() <= fixedRight)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getCharAt(fixedRight)))\r
+ {\r
+ blank = false;\r
+ continue;\r
+ }\r
+ }\r
+ if (blank)\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (fixedRight <= startres)\r
{\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j,sno);\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
\r
- int index = align.findIndex(s);\r
- if (index != -1)\r
- drawChars(index,index+1,lastres);\r
\r
+ // drag to left\r
+ else\r
+ {\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
+\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ seq = sg.getSequenceAt(s);\r
\r
- } else if (res < align.getWidth() && res < lastres)\r
+ for (int j = startres; j < lastres; j++)\r
{\r
- for (int j = res; j < lastres; j++)\r
+ if (seq.getSequence().length() <= j)\r
{\r
- deleteChar(j,res,sno);\r
- startres = res;\r
- }\r
- int index = align.findIndex(s);\r
- if (index != -1)\r
- drawChars(index,index+1,res);\r
+ continue;\r
+ }\r
\r
- }\r
- }\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getSequence().charAt(j)))\r
+ {\r
+ // Not a gap, block edit not valid\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- }\r
- lastres = res;\r
- } else {\r
\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ seq = sg.getSequenceAt(i);\r
\r
- if (res < align.getWidth() && res > lastres) {\r
+ if (insertGap)\r
+ {\r
+ // dragging to the right\r
+ for (int j = lastres; j < startres; j++)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ insertChar(j, seq, fixedRight);\r
+ }\r
+ else\r
+ insertChar(j, seq);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ deleteChar(startres, seq, fixedRight);\r
+ }\r
+ else\r
+ {\r
+ deleteChar(startres, seq);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else /////Editing a single sequence///////////\r
+ {\r
+\r
+ if (insertGap)\r
+ {\r
// dragging to the right\r
- for (int j = lastres; j < res; j++)\r
+ for (int j = lastres; j < startres; j++)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ insertChar(j, seq, fixedRight);\r
+ else\r
+ insertChar(j, seq);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > startres; j--)\r
{\r
- insertChar(j,startseq);\r
- }\r
- drawChars(startseq,startseq+1,lastres);\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ deleteChar(startres, seq, fixedRight);\r
+ }\r
+ else\r
+ {\r
+ deleteChar(startres, seq);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ lastres = startres;\r
+ seqCanvas.repaint();\r
+ }\r
\r
- } else if (res < align.getWidth() && res < lastres) {\r
\r
- // dragging to the left\r
- for (int j = res; j < lastres; j++) {\r
- deleteChar(j,res,startseq);\r
- startres = res;\r
- }\r
- drawChars(startseq,startseq+1,res);\r
- }\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param j DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ void insertChar(int j, SequenceI seq)\r
+ {\r
+ seq.insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
+ }\r
+\r
+ void insertChar(int j, SequenceI seq, int fixedColumn)\r
+ {\r
+ //Find the next gap before the end of the visible region boundary\r
+ //If lastCol > j, theres a boundary after the gap insertion\r
+ int blankColumn = fixedColumn;\r
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
+ {\r
+ //Theres a space, so break and insert the gap\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (blankColumn <= j)\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
+ {\r
+ //Just Checking\r
+ System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));\r
+ return;\r
}\r
- lastres = res;\r
+\r
+ seq.deleteCharAt(blankColumn);\r
+ seq.insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
}\r
\r
- repaint();\r
- return;\r
- }\r
+ void deleteChar(int j, SequenceI seq, int fixedColumn)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+ {\r
+ ap.alignFrame.statusBar.setText(\r
+ "End editing: Tried removing residue " + seq.getCharAt(j));\r
+ return;\r
+ }\r
\r
- public void drawChars(int seqstart, int seqend, int start) {\r
- seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);\r
- repaint();\r
- }\r
+ seq.deleteCharAt(j);\r
+ seq.insertCharAt(fixedColumn, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
+ }\r
\r
- public void insertChar(int j, int seq)\r
- {\r
- align.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param j DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ void deleteChar(int j, SequenceI seq)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+ {\r
+ ap.alignFrame.statusBar.setText(\r
+ "End editing: Tried removing residue " + seq.getCharAt(j));\r
+ return;\r
+ }\r
\r
- public void deleteChar(int j, int res, int sno)\r
- {\r
+ seq.deleteCharAt(j);\r
+ seqEditOccurred = true;\r
+ seqCanvas.repaint();\r
+ }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseEntered(MouseEvent e)\r
+ {\r
+ if(oldSeq < 0)\r
+ oldSeq = 0;\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+ }\r
\r
- if (align.getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||\r
- align.getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||\r
- align.getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseExited(MouseEvent e)\r
{\r
- align.getSequenceAt(sno).deleteCharAt(j);\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (mouseDragging)\r
+ {\r
+ scrollThread = new ScrollThread();\r
+ }\r
}\r
\r
- align.getWidth();\r
- repaint();\r
- }\r
+ public void mouseClicked(MouseEvent evt)\r
+ {}\r
\r
- public void setColourScheme(ColourSchemeI cs)\r
- {\r
- seqCanvas.cs = cs;\r
- seqCanvas.paintFlag = true;\r
- repaint();\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
+ av.setFont(new Font(font.getName(), font.getStyle(), fontSize));\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
- public ColourSchemeI getColourScheme()\r
- {\r
- return seqCanvas.cs;\r
- }\r
+ }\r
\r
\r
-}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
+ void editOccurred()\r
+ {\r
+ if (!seqEditOccurred)\r
+ {\r
+ ap.alignFrame.historyList.pop();\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\r
+\r
+ endEditing();\r
+\r
+ av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void doMousePressedDefineMode(MouseEvent evt)\r
+ {\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
+ oldSeq = seq;\r
+\r
+ startWrapBlock=wrappedBlock;\r
+\r
+ if(av.wrapAlignment && seq>av.alignment.getHeight())\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Cannot edit annotations in wrapped view.",\r
+ "Wrapped view - no edit",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
+ if(seq<0 || res<0)\r
+ return;\r
+\r
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
+\r
+ if ((sequence == null) || (res > sequence.getLength()))\r
+ {\r
+ return;\r
+ }\r
+\r
+ stretchGroup = av.getSelectionGroup();\r
+\r
+ if (stretchGroup == null)\r
+ {\r
+ stretchGroup = av.alignment.findGroup(sequence);\r
+\r
+ if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&\r
+ (res < stretchGroup.getEndRes()))\r
+ {\r
+ av.setSelectionGroup(stretchGroup);\r
+ }\r
+ else\r
+ {\r
+ stretchGroup = null;\r
+ }\r
+ }\r
+ else if (!stretchGroup.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
+\r
+ break;\r
+ }\r
+ }\r
+ }\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
+\r
+ if (stretchGroup == null)\r
+ {\r
+ // define a new group here\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ sg.addSequence(sequence, false);\r
+ av.setSelectionGroup(sg);\r
+ stretchGroup = sg;\r
+\r
+ if (av.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(ap,\r
+ av.getGlobalColourScheme(), "Background");\r
+ }\r
+\r
+ if (av.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
+ }\r
+ else if (javax.swing.SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+\r
+ // edit the properties of existing group\r
+ }\r
+\r
+ if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))\r
+ {\r
+ // Edit end res position of selected group\r
+ changeEndRes = true;\r
+ }\r
+ else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))\r
+ {\r
+ // Edit end res position of selected group\r
+ changeStartRes = true;\r
+ }\r
+\r
+ stretchGroup.getWidth();\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(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
+ }\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
+\r
+ if(y > av.alignment.getHeight())\r
+ {\r
+ y = av.alignment.getHeight() -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.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
+ mouseDragging = true;\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.setEvent(evt);\r
+ }\r
+\r
+ seqCanvas.repaint();\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
git://source.jalview.org / jalview.git / blobdiff