/*\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
+ * 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
\r
package jalview.appletgui;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
+\r
import jalview.datamodel.*;\r
-import java.util.*;\r
import jalview.schemes.*;\r
\r
+import java.util.Vector;\r
\r
-public class SeqPanel extends Panel\r
+public class SeqPanel\r
+ extends Panel implements MouseMotionListener, MouseListener\r
{\r
\r
- public SeqCanvas seqCanvas;\r
- public AlignmentPanel ap;\r
+ public SeqCanvas seqCanvas;\r
+ public AlignmentPanel ap;\r
\r
protected int lastres;\r
protected int startseq;\r
- int startEdit=-1;\r
- int endEdit=-1;\r
\r
protected AlignViewport av;\r
\r
// if character is inserted or deleted, we will need to recalculate the conservation\r
- int seqEditOccurred = -1;\r
+ boolean seqEditOccurred = false;\r
\r
ScrollThread scrollThread = null;\r
boolean mouseDragging = false;\r
-\r
boolean editingSeqs = false;\r
boolean groupEditing = false;\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
+\r
+ StringBuffer keyboardNo1;\r
+ StringBuffer keyboardNo2;\r
\r
+ boolean mouseWheelPressed = false;\r
+ Point lastMousePress;\r
\r
- public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
- this.av = avp;\r
+ public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
+ {\r
+ this.av = avp;\r
\r
- seqCanvas = new SeqCanvas(avp);\r
+ seqCanvas = new SeqCanvas(avp);\r
setLayout(new BorderLayout());\r
add(seqCanvas);\r
\r
ap = p;\r
\r
- seqCanvas.addMouseMotionListener( new MouseMotionAdapter()\r
- {\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- if(av.getWrapAlignment())\r
- return;\r
- doMouseMoved(evt); }\r
+ seqCanvas.addMouseMotionListener(this);\r
+ seqCanvas.addMouseListener(this);\r
\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- if(av.getWrapAlignment())\r
+ seqCanvas.repaint();\r
+ }\r
+\r
+ void endEditing()\r
+ {\r
+ startseq = -1;\r
+ lastres = -1;\r
+ seqEditOccurred = false;\r
+ editingSeqs = false;\r
+ groupEditing = false;\r
+ keyboardNo1 = null;\r
+ keyboardNo2 = 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
+ while (seqCanvas.cursorX < av.startRes)\r
+ {\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
+ 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).removeAllElements();\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+getKeyboardNo(keyboardNo1));\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+getKeyboardNo(keyboardNo1);\r
+ editSequence(false, seqCanvas.cursorX);\r
+ editOccurred();\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
+ 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
+\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
+ }\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ lastMousePress = evt.getPoint();\r
+\r
+ if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==\r
+ InputEvent.BUTTON2_MASK)\r
+ {\r
+ mouseWheelPressed = true;\r
return;\r
- if( editingSeqs )\r
- doMouseDragged(evt);\r
- else\r
- doMouseDraggedDefineMode(evt);\r
- }\r
- });\r
+ }\r
\r
- seqCanvas.addMouseListener( new MouseAdapter()\r
- {\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if(av.getWrapAlignment())\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
- if(editingSeqs)\r
- doMouseReleased(evt);\r
- else\r
- doMouseReleasedDefineMode(evt);\r
+ }\r
\r
- }\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if(av.getWrapAlignment())\r
+\r
+ int seq = findSeq(evt);\r
+ int res = findRes(evt);\r
+\r
+ if(seq<0 || res<0)\r
return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
- {\r
- if(evt.isAltDown() || evt.isControlDown())\r
- groupEditing = true;\r
\r
- editingSeqs = true;\r
- doMousePressed(evt);\r
- }\r
- else\r
- doMousePressedDefineMode(evt);\r
- }\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || editingSeqs)\r
- return;\r
- doMouseExitedDefineMode(evt);\r
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
+ av.alignment, HistoryItem.EDIT));\r
\r
- }\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || editingSeqs)\r
- return;\r
- doMouseEnteredDefineMode(evt);\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
- });\r
- seqCanvas.repaint();\r
+ return;\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt){}\r
+\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
+ editOccurred();\r
+\r
+ endEditing();\r
+ ap.repaint();\r
}\r
\r
+ int startWrapBlock=-1;\r
+ int wrappedBlock=-1;\r
+ int findRes(MouseEvent evt)\r
+ {\r
+ int res = 0;\r
+ int x = evt.getX();\r
\r
- public void doMouseReleased(MouseEvent evt) {\r
+ if (av.wrapAlignment)\r
+ {\r
\r
- if(seqEditOccurred>-1)\r
- editOccurred(seqEditOccurred);\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- startseq = -1;\r
- lastres = -1;\r
- seqEditOccurred = -1;\r
- editingSeqs = false;\r
- groupEditing = false;\r
- ap.repaint();\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap + seqCanvas.getAnnotationHeight();\r
+\r
+ int y = evt.getY();\r
+ y -= hgap;\r
+ x -= seqCanvas.LABEL_WEST;\r
+\r
+\r
+ int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);\r
+\r
+ wrappedBlock = y / cHeight;\r
+ wrappedBlock += av.getStartRes() / cwidth;\r
+\r
+ res = wrappedBlock * cwidth + x / av.getCharWidth();\r
+\r
+ }\r
+ else\r
+ {\r
+ res = (x / av.getCharWidth()) + av.getStartRes();\r
}\r
\r
- public void doMousePressed(MouseEvent evt) {\r
- ap.alignFrame.addHistoryItem( new HistoryItem(\r
- "Edit Sequence",av.alignment, HistoryItem.EDIT));\r
- int seq;\r
- int res;\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
+ 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
- int x = evt.getX();\r
- int y = evt.getY();\r
+ y -= hgap;\r
\r
- res = x/av.getCharWidth() + av.getStartRes();\r
- seq = y/av.getCharHeight() + av.getStartSeq();\r
+ seq = Math.min( (y % cHeight) / av.getCharHeight(),\r
+ av.alignment.getHeight() -1);\r
+ if(seq<0)\r
+ seq = 0;\r
+ }\r
+ else\r
+ {\r
+ seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),\r
+ av.alignment.getHeight() -1);\r
+ if(seq<0)\r
+ seq = 0;\r
+ }\r
+\r
+ return seq;\r
+ }\r
+\r
+\r
+ public void doMousePressed(MouseEvent evt)\r
+ {\r
+ ap.alignFrame.addHistoryItem(new HistoryItem(\r
+ "Edit Sequence", av.alignment, HistoryItem.EDIT));\r
+\r
+ int seq = findSeq(evt);\r
+ int res = findRes(evt);\r
\r
if (seq < av.getAlignment().getHeight() &&\r
res < av.getAlignment().getSequenceAt(seq).getLength())\r
return;\r
}\r
\r
- public void doMouseMoved(MouseEvent evt)\r
+ public void mouseMoved(MouseEvent evt)\r
{\r
- int res=0, seq=0;\r
- int x = evt.getX();\r
- int y = evt.getY();\r
- if(av.wrapAlignment)\r
- {\r
- y -= 2*av.charHeight;\r
- int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
\r
+ if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)\r
+ {\r
+ return;\r
+ }\r
\r
- res = (int)((y/chunkHeight)*(getSize().width/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
+ if (res > sequence.getLength())\r
+ {\r
+ return;\r
+ }\r
\r
- y %= chunkHeight;\r
- seq = y / av.getCharHeight() + av.getStartSeq();\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
- res = x / av.getCharWidth() + av.getStartRes();\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
+ if(obj!=null)\r
+ text.append(" Residue: ");\r
}\r
\r
+ if (obj != null)\r
+ {\r
+ if (obj != "")\r
+ {\r
+ text.append(obj + " (" + sequence.findPosition(res) + ")");\r
+ }\r
+ }\r
\r
- if(seq>=av.getAlignment().getHeight())\r
- return;\r
-\r
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
- if(res>sequence.getLength())\r
- return;\r
-\r
- Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;\r
- String aa = "";\r
- if(obj!=null)\r
- aa = obj.toString();\r
-\r
- StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());\r
- if(aa!="")\r
- text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");\r
+ if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
+ {\r
+ seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
+ }\r
\r
ap.alignFrame.statusBar.setText(text.toString());\r
\r
+\r
// use aa to see if the mouse pointer is on a\r
- if( av.showSequenceFeatures)\r
+ if (av.showSequenceFeatures\r
+ && sequence.getSequenceFeatures()!=null\r
+ && av.featuresDisplayed!=null)\r
{\r
- Vector features = sequence.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- StringBuffer sbuffer = new StringBuffer();\r
-\r
+ StringBuffer featureText = new StringBuffer();\r
+ Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));\r
\r
- while (e.hasMoreElements())\r
+ int index = 0;\r
+ while (index < allFeatures.size())\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- if (sf.getStart() <= sequence.findPosition(res) &&\r
- sf.getEnd() >= sequence.findPosition(res))\r
+ SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);\r
+\r
+ featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);\r
+\r
+ if (sf.getDescription() != null)\r
+ featureText.append(" " + sf.getDescription());\r
+\r
+ if (sf.getValue("status") != null )\r
{\r
- if(sbuffer.length()>0)\r
- sbuffer.append("; ");\r
- sbuffer.append(sf.getType() + " " + sf.getDescription());\r
- if(sf.getStatus().length()>0)\r
- sbuffer.append(" ("+sf.getStatus()+")");\r
+ featureText.append(" (" + sf.getValue("status") + ")");\r
}\r
+ featureText.append("\n");\r
\r
+ index++;\r
}\r
- }\r
\r
\r
+ if (tooltip == null)\r
+ tooltip = new Tooltip(featureText.toString(), seqCanvas);\r
+ else\r
+ tooltip.setTip(featureText.toString());\r
+\r
+ tooltip.repaint();\r
+\r
+ }\r
}\r
\r
- public void doMouseDragged(MouseEvent evt) {\r
+ Vector getAllFeaturesAtRes(SequenceI seq, int res)\r
+ {\r
+ Vector allFeatures = new Vector();\r
+ int index = 0;\r
+ if(seq.getSequenceFeatures()!=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
- // If we're dragging we're editing\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- if (res < 0)\r
- res = 0;\r
+ Tooltip tooltip;\r
\r
- if (lastres == -1 || lastres == res)\r
- return;\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (mouseWheelPressed)\r
+ {\r
+ int oldWidth = av.charWidth;\r
\r
- boolean dragRight = true;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
- dragRight = false;\r
+ //Which is bigger, left-right or up-down?\r
+ if (Math.abs(evt.getY() - lastMousePress.y)\r
+ > Math.abs(evt.getX() - lastMousePress.x))\r
+ {\r
+ int fontSize = av.font.getSize();\r
\r
+ if (evt.getY() < lastMousePress.y && av.charHeight > 1)\r
+ {\r
+ fontSize--;\r
+ }\r
+ else if (evt.getY() > lastMousePress.y)\r
+ {\r
+ fontSize++;\r
+ }\r
\r
- if (res != lastres)\r
- {\r
- // Group editing\r
- if (groupEditing)\r
- {\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(sg==null)\r
- {\r
- lastres=-1;\r
- return;\r
- }\r
\r
- // drag to right\r
- if(dragRight)\r
- sg.setEndRes(sg.getEndRes() + (res-lastres));\r
-\r
- // drag to left\r
- else\r
- {\r
- /// Are we able to delete?\r
- // ie are all columns blank?\r
- boolean deleteAllowed = false;\r
- for (int s = 0; s < sg.getSize(); s++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(s);\r
- for (int j=res; j<lastres; j++)\r
- {\r
- if(seq.getSequence().length()<=j)\r
- continue;\r
-\r
- if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
- {\r
- // Not a gap, block edit not valid\r
- res=j+1;\r
- deleteAllowed = false;\r
- continue;\r
- }\r
- deleteAllowed = true;\r
- }\r
- }\r
-\r
- if(!deleteAllowed)\r
- {\r
- lastres = -1;\r
- return;\r
- }\r
-\r
- sg.setEndRes(sg.getEndRes() - (lastres-res));\r
- }\r
-\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI s = sg.getSequenceAt(i);\r
- int k = av.alignment.findIndex(s);\r
-\r
- // drag to right\r
- if (dragRight)\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, k);\r
-\r
- // drag to left\r
- else\r
- {\r
- for (int j = res; j < lastres; j++)\r
- {\r
- if(s.getLength()>j)\r
- deleteChar(res, k);\r
- }\r
- }\r
- }\r
- }\r
- else /////Editing a single sequence///////////\r
- {\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
- {\r
- // dragging to the right\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, startseq);\r
- }\r
- else if (res < av.getAlignment().getWidth() && res < lastres)\r
- {\r
- // dragging to the left\r
- for (int j = lastres; j > res; j--)\r
- {\r
- if( jalview.util.Comparison.isGap(\r
- av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
-\r
- deleteChar(res, startseq);\r
- else\r
- {\r
-\r
- break;\r
- }\r
- }\r
- }\r
+ if(fontSize<1)\r
+ fontSize = 1;\r
\r
- }\r
- }\r
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));\r
+ av.charWidth = oldWidth;\r
+ }\r
+ else\r
+ {\r
+ if (evt.getX() < lastMousePress.x && av.charWidth > 1)\r
+ {\r
+ av.charWidth--;\r
+ }\r
+ else if (evt.getX() > lastMousePress.x)\r
+ {\r
+ av.charWidth++;\r
+ }\r
\r
- endEdit = res;\r
- lastres = res;\r
- seqCanvas.repaint();\r
+ if(av.charWidth<1)\r
+ {\r
+ av.charWidth = 1;\r
+ }\r
+ }\r
+\r
+ ap.fontChanged();\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ av.validCharWidth = fm.charWidth('M') <= av.charWidth;\r
+\r
+ lastMousePress = evt.getPoint();\r
+\r
+ ap.repaint();\r
+ ap.annotationPanel.image = null;\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
- 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
- seqCanvas.repaint();\r
+ if ((lastres == -1) || (lastres == res))\r
+ {\r
+ return;\r
}\r
\r
- public void insertChar(int j, int seq)\r
+ if ( (res < av.getAlignment().getWidth()) && (res < lastres))\r
{\r
- av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred=seq;\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
- public void deleteChar(int j, int seq)\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
+ 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
+ || (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
- av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
- seqEditOccurred=seq;\r
- av.alignment.getWidth();\r
- repaint();\r
+ fixedLeft = sg.getStartRes();\r
+ fixedRight = sg.getEndRes();\r
+\r
+ if ( (startres < fixedLeft && lastres >= fixedLeft)\r
+ || (startres >= fixedLeft && lastres < fixedLeft)\r
+ || (startres > fixedRight && lastres <=fixedRight)\r
+ || (startres <= fixedRight && lastres > fixedRight))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ if (fixedLeft > startres)\r
+ {\r
+ fixedRight = fixedLeft - 1;\r
+ fixedLeft = 0;\r
+ }\r
+ else if (fixedRight < startres)\r
+ {\r
+ fixedLeft = fixedRight;\r
+ fixedRight = -1;\r
+ }\r
+ }\r
+\r
+\r
+ if(av.hasHiddenColumns )\r
+ {\r
+ fixedColumns = true;\r
+ int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);\r
+ int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);\r
+\r
+ if ( (insertGap && startres > y1 && lastres < y1)\r
+ || (!insertGap && startres < y2 && lastres > y2))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");\r
+ //Selection spans a hidden region\r
+ if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))\r
+ {\r
+ if(startres>=y2)\r
+ {\r
+ fixedLeft = y2;\r
+ }\r
+ else\r
+ {\r
+ fixedRight = y2 - 1;\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ if (groupEditing)\r
+ {\r
+ // drag to right\r
+ if (insertGap)\r
+ {\r
+ //If the user has selected the whole sequence, and is dragging to\r
+ // the right, we can still extend the alignment and selectionGroup\r
+ if( sg.getStartRes() == 0\r
+ && sg.getEndRes() == fixedRight\r
+ && sg.getEndRes() == av.alignment.getWidth()-1\r
+ )\r
+ {\r
+ sg.setEndRes(av.alignment.getWidth() + startres - lastres);\r
+ fixedRight = sg.getEndRes();\r
+ }\r
+\r
+ // Is it valid with fixed columns??\r
+ // Find the next gap before the end\r
+ // of the visible region boundary\r
+ boolean blank = false;\r
+ for (fixedRight = fixedRight;\r
+ fixedRight > lastres;\r
+ fixedRight--)\r
+ {\r
+ blank = true;\r
+ for (int s = 0; s < sg.getSize(true); s++)\r
+ {\r
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
+ for (int j = 0; j < startres - lastres; j++)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getCharAt(fixedRight - j)))\r
+ {\r
+ blank = false;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if (blank)\r
+ break;\r
+ }\r
+\r
+ if (!blank)\r
+ {\r
+ if(sg.getSize(false) == av.alignment.getHeight() )\r
+ {\r
+ if((av.hasHiddenColumns\r
+ && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+\r
+ int alWidth = av.alignment.getWidth();\r
+ if(av.hasHiddenRows)\r
+ {\r
+ int hwidth = av.alignment.getHiddenSequences().getWidth();\r
+ if(hwidth>alWidth)\r
+ alWidth = hwidth;\r
+ }\r
+ //We can still insert gaps if the selectionGroup\r
+ //contains all the sequences\r
+ sg.setEndRes(sg.getEndRes()+startres-lastres);\r
+ fixedRight = alWidth+startres-lastres;\r
+ }\r
+ else\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ // drag to left\r
+ else if(!insertGap)\r
+ {\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
+\r
+ for (int s = 0; s < sg.getSize(true); s++)\r
+ {\r
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);\r
+\r
+ for (int j = startres; j < lastres; j++)\r
+ {\r
+ if (seq.getSequence().length() <= j)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getSequence().charAt(j)))\r
+ {\r
+ // Not a gap, block edit not valid\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ for (int i = 0; i < sg.getSize(true); i++)\r
+ {\r
+ seq = (SequenceI) sg.getSequences(true).elementAt(i);\r
+\r
+ if (insertGap)\r
+ {\r
+ // dragging to the right\r
+ for (int j = lastres; j < startres; j++)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ insertChar(j, seq, fixedRight);\r
+ }\r
+ else\r
+ insertChar(j, seq);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ deleteChar(startres, seq, fixedRight);\r
+ }\r
+ else\r
+ {\r
+ deleteChar(startres, seq);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else /////Editing a single sequence///////////\r
+ {\r
+ if (insertGap)\r
+ {\r
+ // dragging to the right\r
+ for (int j = lastres; j < startres; j++)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ insertChar(j, seq, fixedRight);\r
+ }\r
+ else\r
+ insertChar(j, seq);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ if (fixedColumns && fixedRight != -1)\r
+ {\r
+ deleteChar(startres, seq, fixedRight);\r
+ }\r
+ else\r
+ {\r
+ deleteChar(startres, seq);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ lastres = startres;\r
+ seqCanvas.repaint();\r
}\r
\r
\r
- void editOccurred(int i)\r
- {\r
- if(endEdit==startEdit)\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
- ap.alignFrame.historyList.pop();\r
- ap.alignFrame.updateEditMenuBar();\r
+ seq.insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
}\r
\r
- av.updateConservation();\r
- av.updateConsensus();\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
+\r
+ seq.deleteCharAt(blankColumn);\r
+ seq.insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
+ }\r
\r
- // Y O Y CLUSTALX\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme)\r
+ void deleteChar(int j, SequenceI seq, int fixedColumn)\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
- if(ccs.cs instanceof ClustalxColourScheme)\r
- {\r
- jalview.analysis.Conservation c = new jalview.analysis.Conservation\r
- ("All",\r
- ResidueProperties.propHash, 3,\r
- av.alignment.getSequences(), 0,\r
- av.alignment.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
-\r
- ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;\r
- cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());\r
- ccs = new ConservationColourScheme(c, cxs);\r
- av.setGlobalColourScheme(ccs);\r
- }\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+ {\r
+ ap.alignFrame.statusBar.setText(\r
+ "End editing: Tried removing residue " + seq.getCharAt(j));\r
+ return;\r
+ }\r
+\r
+ seq.deleteCharAt(j);\r
+ seq.insertCharAt(fixedColumn, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
}\r
\r
- if(cs instanceof ClustalxColourScheme)\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
- ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- av.setGlobalColourScheme(cs);\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+ {\r
+ ap.alignFrame.statusBar.setText(\r
+ "End editing: Tried removing residue " + seq.getCharAt(j));\r
+ return;\r
+ }\r
+\r
+ seq.deleteCharAt(j);\r
+ seqEditOccurred = true;\r
+ seqCanvas.repaint();\r
}\r
\r
+ /**\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
- }\r
+ endEditing();\r
+\r
+ av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
+\r
+ }\r
\r
//////////////////////////////////////////\r
/////Everything below this is for defining the boundary of the rubberband\r
//////////////////////////////////////////\r
- int oldSeq = -1;\r
public void doMousePressedDefineMode(MouseEvent evt)\r
{\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
oldSeq = seq;\r
+ startWrapBlock=wrappedBlock;\r
+\r
+ if(seq==-1)\r
+ return;\r
\r
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
\r
- if(sequence==null || res>sequence.getLength())\r
+ if (sequence == null || res > sequence.getLength())\r
+ {\r
return;\r
+ }\r
\r
stretchGroup = av.getSelectionGroup();\r
\r
- if(stretchGroup == null)\r
- {\r
- stretchGroup = av.alignment.findGroup( sequence );\r
- if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
- av.setSelectionGroup(stretchGroup);\r
- else\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
- for (int i = 0; i < allGroups.length; i++)\r
- if (allGroups[i].getStartRes() <= res &&\r
- allGroups[i].getEndRes() >= res)\r
- {\r
- stretchGroup = allGroups[i];\r
- av.setSelectionGroup(stretchGroup);\r
- break;\r
- }\r
- }\r
+ if (stretchGroup == null)\r
+ {\r
+ stretchGroup = av.alignment.findGroup(sequence);\r
+ if (stretchGroup != null && res > stretchGroup.getStartRes() &&\r
+ res < stretchGroup.getEndRes())\r
+ {\r
+ av.setSelectionGroup(stretchGroup);\r
+ }\r
+ else\r
+ {\r
+ stretchGroup = null;\r
+ }\r
+ }\r
\r
- if(stretchGroup==null)\r
+ else if (!stretchGroup.getSequences(false).contains(sequence)\r
+ || stretchGroup.getStartRes() > res\r
+ || stretchGroup.getEndRes() < res)\r
{\r
- // define a new group here\r
- SequenceGroup sg = new SequenceGroup();\r
- sg.setStartRes(res);\r
- sg.setEndRes(res);\r
- sg.addSequence( sequence );\r
- av.setSelectionGroup( sg );\r
- stretchGroup = sg;\r
+ stretchGroup = null;\r
\r
- if(av.getConservationSelected())\r
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
- if(av.getAbovePIDThreshold())\r
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\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
+ av.setSelectionGroup(stretchGroup);\r
}\r
\r
+\r
// DETECT RIGHT MOUSE BUTTON IN AWT\r
- else if( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )\r
+ if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
+ InputEvent.BUTTON3_MASK)\r
{\r
- APopupMenu popup = new APopupMenu(ap, null);\r
+ Vector allFeatures = getAllFeaturesAtRes(sequence,\r
+ sequence.findPosition(res));\r
+\r
+ Vector links = null;\r
+ if(allFeatures!=null)\r
+ {\r
+ for (int i = 0; i < allFeatures.size(); i++)\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);\r
+ if (sf.links != null)\r
+ {\r
+ links = new Vector();\r
+ for (int j = 0; j < sf.links.size(); j++)\r
+ {\r
+ links.addElement(sf.links.elementAt(j));\r
+ }\r
+ }\r
+ }\r
+ }\r
+ APopupMenu popup = new APopupMenu(ap, null, links);\r
this.add(popup);\r
popup.show(this, evt.getX(), evt.getY());\r
+ ap.repaint();\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 && stretchGroup.getEndRes()==res)\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
+ //Only if left mouse button do we want to change group sizes\r
\r
- else if(stretchGroup!=null && stretchGroup.getStartRes()==res)\r
- // Edit end res position of selected group\r
- changeStartRes = true;\r
+ if (stretchGroup == null)\r
+ {\r
+ // define a new group here\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ sg.addSequence(sequence, false);\r
+ av.setSelectionGroup(sg);\r
+ stretchGroup = sg;\r
+\r
+ if (av.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
+ if (av.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
\r
+ }\r
}\r
\r
- boolean changeEndSeq = false;\r
- boolean changeStartSeq = false;\r
- boolean changeEndRes = false;\r
- boolean changeStartRes = false;\r
- SequenceGroup stretchGroup = null;\r
-\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
- mouseDragging = false;\r
-\r
- if(stretchGroup==null)\r
- return;\r
-\r
- if(stretchGroup.cs instanceof ClustalxColourScheme)\r
+ if (stretchGroup == null)\r
{\r
- stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());\r
- seqCanvas.repaint();\r
+ return;\r
}\r
\r
- else if(stretchGroup.cs instanceof ConservationColourScheme)\r
+ if(stretchGroup.cs!=null)\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
- stretchGroup.cs = ccs;\r
- SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
-\r
- seqCanvas.repaint();\r
- }\r
- else\r
- {\r
- if(stretchGroup.cs !=null)\r
+ if (stretchGroup.cs instanceof ClustalxColourScheme)\r
{\r
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\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
-\r
-\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
+ PaintRefresher.Refresh(av.alignment);\r
ap.repaint();\r
}\r
\r
-\r
- boolean remove = false;\r
public void doMouseDraggedDefineMode(MouseEvent evt)\r
{\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+ int res = findRes(evt);\r
+ int y = findSeq(evt);\r
\r
- if(stretchGroup==null)\r
+ if(wrappedBlock!=startWrapBlock)\r
return;\r
\r
- if(res>av.alignment.getWidth())\r
- res = av.alignment.getWidth()-1;\r
+ if (stretchGroup == null)\r
+ {\r
+ return;\r
+ }\r
\r
+ mouseDragging = true;\r
\r
- if(stretchGroup.getEndRes()==res)\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
\r
- else if(stretchGroup.getStartRes()==res)\r
- // Edit start res position of selected group\r
- changeStartRes = true;\r
+ if(y > av.alignment.getHeight())\r
+ {\r
+ y = av.alignment.getHeight() -1;\r
+ }\r
\r
+ if(res>av.alignment.getWidth())\r
+ res = av.alignment.getWidth()-1;\r
\r
- if(res<av.getStartRes())\r
- res = av.getStartRes();\r
- else if(res>av.getEndRes())\r
- res = av.getEndRes();\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(changeEndRes)\r
- {\r
- if(res>stretchGroup.getStartRes()-1)\r
- stretchGroup.setEndRes( res );\r
- }\r
- else if(changeStartRes)\r
- {\r
- if(res<stretchGroup.getEndRes()+1)\r
- stretchGroup.setStartRes( res );\r
- }\r
+ if (res < 0)\r
+ {\r
+ res = 0;\r
+ }\r
\r
- int dragDirection = 0;\r
- if (y > oldSeq)\r
- dragDirection = 1;\r
- else if (y < oldSeq)\r
- dragDirection = -1;\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
- while (y != oldSeq && oldSeq>0 && 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
+ int dragDirection = 0;\r
\r
- oldSeq += dragDirection;\r
- Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+ if (y > oldSeq)\r
+ {\r
+ dragDirection = 1;\r
+ }\r
+ else if (y < oldSeq)\r
+ {\r
+ dragDirection = -1;\r
+ }\r
\r
- if (stretchGroup.sequences.contains(nextSeq))\r
+\r
+ while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))\r
{\r
- stretchGroup.deleteSequence(seq);\r
- stretchGroup.deleteSequence(nextSeq);\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
- else\r
+\r
+ if(oldSeq < 0)\r
+ oldSeq = -1;\r
+\r
+\r
+ if(res>av.endRes || res<av.startRes\r
+ || y<av.startSeq || y>av.endSeq)\r
{\r
- if(seq!=null)\r
- stretchGroup.addSequence(seq);\r
- stretchGroup.addSequence(nextSeq);\r
+ mouseExited(evt);\r
}\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.setEvent(evt);\r
+ }\r
+\r
+ seqCanvas.repaint();\r
}\r
- oldSeq = y;\r
- mouseDragging = true;\r
- if(scrollThread!=null)\r
- scrollThread.setEvent(evt);\r
\r
- seqCanvas.repaint();\r
- }\r
+ public void mouseEntered(MouseEvent e)\r
+ {\r
+ if (oldSeq < 0)\r
+ oldSeq = 0;\r
\r
- public void doMouseEnteredDefineMode(MouseEvent e)\r
- {\r
- if (scrollThread != null)\r
- scrollThread.running = false;\r
- }\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+ }\r
\r
- public void doMouseExitedDefineMode(MouseEvent e)\r
+ public void mouseExited(MouseEvent e)\r
{\r
if (av.getWrapAlignment())\r
+ {\r
return;\r
+ }\r
\r
- if(mouseDragging)\r
+ if (mouseDragging && scrollThread==null)\r
+ {\r
scrollThread = new ScrollThread();\r
-\r
+ }\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
// this class allows scrolling off the bottom of the visible alignment\r
- class ScrollThread extends Thread\r
+ class ScrollThread\r
+ extends Thread\r
{\r
MouseEvent evt;\r
boolean running = false;\r
running = true;\r
while (running)\r
{\r
- if(evt!=null)\r
+\r
+ if (evt != null)\r
{\r
\r
if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
+ {\r
running = ap.scrollUp(true);\r
+ }\r
\r
if (mouseDragging && evt.getY() >= getSize().height &&\r
av.alignment.getHeight() > av.getEndSeq())\r
+ {\r
running = ap.scrollUp(false);\r
+ }\r
\r
if (mouseDragging && evt.getX() < 0)\r
- running = ap.scrollRight(true);\r
+ {\r
+ running = ap.scrollRight(false);\r
+ }\r
\r
else if (mouseDragging && evt.getX() >= getSize().width)\r
- running = ap.scrollRight(false);\r
+ {\r
+ running = ap.scrollRight(true);\r
+ }\r
}\r
\r
try\r
{}\r
}\r
}\r
-}\r
-\r
-\r
+ }\r
\r
}\r
-\r
-\r
-\r
-\r
git://source.jalview.org / jalview.git / blobdiff