*/\r
package jalview.gui;\r
\r
-import jalview.analysis.*;\r
-\r
import jalview.datamodel.*;\r
\r
import jalview.schemes.*;\r
SequenceGroup stretchGroup = null;\r
boolean remove = false;\r
\r
+ boolean mouseWheelPressed = false;\r
+\r
/**\r
* Creates a new SeqPanel object.\r
*\r
\r
ap = p;\r
\r
+\r
addMouseMotionListener(new MouseMotionAdapter()\r
{\r
public void mouseMoved(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment())\r
+ doMouseMoved(evt);\r
+ if (editingSeqs)\r
{\r
- return;\r
+ // This is because MacOSX creates a mouseMoved\r
+ // If control is down\r
+ if(!av.isDataset())\r
+ doMouseDragged(evt);\r
}\r
-\r
- doMouseMoved(evt);\r
}\r
\r
public void mouseDragged(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
-\r
if (editingSeqs)\r
{\r
+ if(!av.isDataset())\r
doMouseDragged(evt);\r
}\r
else\r
{\r
+ if(!av.isDataset())\r
doMouseDraggedDefineMode(evt);\r
}\r
}\r
});\r
\r
- addMouseListener(new MouseAdapter()\r
- {\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
+ addMouseWheelListener(new MouseWheelListener()\r
+ {\r
+ public void mouseWheelMoved(MouseWheelEvent e)\r
+ {\r
+\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
+ }\r
+ });\r
+\r
+\r
+ if(!av.isDataset())\r
+ {\r
+ addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ mouseWheelPressed = false;\r
+\r
+ if (editingSeqs)\r
+ {\r
+ doMouseReleased(evt);\r
+ }\r
+ else\r
+ {\r
+ doMouseReleasedDefineMode(evt);\r
+ }\r
+ }\r
+\r
+ public void mousePressed(MouseEvent evt)\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
+ }\r
+\r
+ editingSeqs = true;\r
+ doMousePressed(evt);\r
+ }\r
+ else\r
+ {\r
+ doMousePressedDefineMode(evt);\r
+ }\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ if (editingSeqs)\r
+ {\r
+ return;\r
+ }\r
+\r
+ doMouseExitedDefineMode(evt);\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ if (editingSeqs)\r
+ {\r
+ return;\r
+ }\r
+\r
+ doMouseEnteredDefineMode(evt);\r
+ }\r
+ });\r
+ }\r
+ }\r
\r
- if (editingSeqs)\r
- {\r
- doMouseReleased(evt);\r
- }\r
- else\r
- {\r
- doMouseReleasedDefineMode(evt);\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 mousePressed(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
+ if (av.wrapAlignment)\r
+ {\r
\r
- if (evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
- {\r
- if (evt.isAltDown() || evt.isControlDown())\r
- {\r
- groupEditing = true;\r
- }\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- editingSeqs = true;\r
- doMousePressed(evt);\r
- }\r
- else\r
- {\r
- doMousePressedDefineMode(evt);\r
- }\r
- }\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap + seqCanvas.getAnnotationHeight();\r
\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || editingSeqs)\r
- {\r
- return;\r
- }\r
+ int y = evt.getY();\r
+ y -= hgap;\r
+ x -= seqCanvas.LABEL_WEST;\r
\r
- doMouseExitedDefineMode(evt);\r
- }\r
\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || editingSeqs)\r
- {\r
- return;\r
- }\r
+ int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());\r
\r
- doMouseEnteredDefineMode(evt);\r
- }\r
- });\r
+ wrappedBlock = y / cHeight;\r
+ wrappedBlock += av.getStartRes() / cwidth;\r
+\r
+ res = wrappedBlock * cwidth + x / av.getCharWidth();\r
+\r
+ }\r
+ else\r
+ {\r
+ res = (x / av.getCharWidth()) + av.getStartRes();\r
}\r
\r
+ return res;\r
+\r
+ }\r
+\r
+ int findSeq(MouseEvent evt)\r
+ {\r
+\r
+ int seq = 0;\r
+ int y = evt.getY();\r
+\r
+ if (av.wrapAlignment)\r
+ {\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
+\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap + seqCanvas.getAnnotationHeight();\r
+\r
+ y -= hgap;\r
+\r
+ seq = ( (y % cHeight) / av.getCharHeight());\r
+ }\r
+ else\r
+ {\r
+ seq = (y / av.getCharHeight()) + av.getStartSeq();\r
+ }\r
+\r
+ return seq;\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public void doMousePressed(MouseEvent evt)\r
{\r
- ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
- av.alignment, HistoryItem.EDIT));\r
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
+ av.alignment, HistoryItem.EDIT));\r
\r
- int seq;\r
- int res;\r
-\r
- int x = evt.getX();\r
- int y = evt.getY();\r
+ int seq = findSeq(evt);\r
+ int res = findRes(evt);\r
\r
- res = (x / av.getCharWidth()) + av.getStartRes();\r
- seq = (y / av.getCharHeight()) + av.getStartSeq();\r
+ if(seq<0 || res<0)\r
+ return;\r
\r
if ((seq < av.getAlignment().getHeight()) &&\r
(res < av.getAlignment().getSequenceAt(seq).getLength()))\r
*/\r
public void doMouseMoved(MouseEvent evt)\r
{\r
- int res = 0;\r
- int seq = 0;\r
- int x = evt.getX();\r
- int y = evt.getY();\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
\r
- if (av.wrapAlignment)\r
- {\r
- y -= (2 * av.charHeight);\r
+ if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())\r
+ return;\r
\r
- int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
\r
- res = (int) ((y / chunkHeight) * (getWidth() / av.charWidth)) +\r
- (x / av.getCharWidth()) + av.getStartRes();\r
+ if (res > sequence.getLength())\r
+ {\r
+ return;\r
+ }\r
\r
- y %= chunkHeight;\r
- seq = (y / av.getCharHeight()) + av.getStartSeq();\r
- }\r
- else\r
- {\r
- res = (x / av.getCharWidth()) + av.getStartRes();\r
- seq = (y / av.getCharHeight()) + av.getStartSeq();\r
- }\r
+ if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
+ {\r
+ seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
+ }\r
\r
- if (seq >= av.getAlignment().getHeight())\r
- {\r
- return;\r
- }\r
\r
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
+ sequence.getName());\r
\r
- if (res > sequence.getLength())\r
+ Object obj = null;\r
+ if (av.alignment.isNucleotide())\r
{\r
- return;\r
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
+ "");\r
+ if(obj!=null)\r
+ text.append(" Nucleotide: ");\r
}\r
-\r
- Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +\r
- "");\r
- String aa = "";\r
-\r
- if (obj != null)\r
+ else\r
{\r
- aa = obj.toString();\r
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
+ if(obj!=null)\r
+ text.append(" Residue: ");\r
}\r
\r
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
- sequence.getName());\r
-\r
- if (aa != "")\r
+ if (obj != null)\r
{\r
- text.append(" Residue: " + aa + " (" +\r
- av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
+\r
+ if (obj != "")\r
+ {\r
+ text.append( obj + " (" +\r
+ av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
+ }\r
}\r
\r
ap.alignFrame.statusBar.setText(text.toString());\r
// use aa to see if the mouse pointer is on a\r
if (av.showSequenceFeatures)\r
{\r
- Vector features = sequence.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- StringBuffer sbuffer = new StringBuffer();\r
-\r
- while (e.hasMoreElements())\r
+ Vector features = sequence.getDatasetSequence().getSequenceFeatures();\r
+ if(features!=null)\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ StringBuffer sbuffer = new StringBuffer("<html>");\r
\r
- if ((sf.getStart() <= sequence.findPosition(res)) &&\r
- (sf.getEnd() >= sequence.findPosition(res)))\r
+ for (int i = 0; i < features.size(); i++)\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) features.elementAt(i);\r
+\r
+ if ( (sf.getBegin() <= sequence.findPosition(res)) &&\r
+ (sf.getEnd() >= sequence.findPosition(res)))\r
{\r
- if (sbuffer.length() > 0)\r
+ if (sf.getType().equals("disulfide bond"))\r
+ {\r
+ if (sf.getBegin() == sequence.findPosition(res)\r
+ || sf.getEnd() == sequence.findPosition(res))\r
{\r
- sbuffer.append("; ");\r
+ if (sbuffer.length() > 6)\r
+ sbuffer.append("<br>");\r
+ sbuffer.append("disulfide bond " + sf.getBegin() + ":" +\r
+ sf.getEnd());\r
}\r
-\r
- sbuffer.append(sf.getType() + " " + sf.getDescription());\r
-\r
- if (sf.getStatus().length() > 0)\r
+ }\r
+ else\r
+ {\r
+ if (sbuffer.length() > 6)\r
+ sbuffer.append("<br>");\r
+ sbuffer.append(sf.getType());\r
+ if (sf.getDescription() != null)\r
+ sbuffer.append(" " + sf.getDescription());\r
+\r
+ if (sf.getStatus() != null)\r
{\r
- sbuffer.append(" (" + sf.getStatus() + ")");\r
+ sbuffer.append(" (" + sf.getStatus() + ")");\r
}\r
+ }\r
}\r
- }\r
\r
- this.setToolTipText(sbuffer.toString());\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
public void doMouseDragged(MouseEvent evt)\r
{\r
// If we're dragging we're editing\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+ int res = findRes(evt);\r
\r
if (res < 0)\r
{\r
*/\r
void editOccurred(int i)\r
{\r
- if (endEdit == startEdit)\r
- {\r
- ap.alignFrame.historyList.pop();\r
- ap.alignFrame.updateEditMenuBar();\r
- }\r
-\r
- av.updateConservation();\r
- av.updateConsensus();\r
-\r
- // Y O Y CLUSTALX\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
-\r
- if (av.getSelectionGroup() != null)\r
- {\r
- av.getSelectionGroup().recalcConservation();\r
- }\r
-\r
- if (cs.conservationApplied())\r
- {\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, av.alignment.getSequences(),\r
- 0, av.alignment.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
+ if (endEdit == startEdit)\r
+ {\r
+ ap.alignFrame.historyList.pop();\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\r
\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
- cxs.resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- cs.setConservation(c);\r
- av.setGlobalColourScheme(cs);\r
- }\r
- else\r
- {\r
- cs.setConservation(c);\r
- av.setGlobalColourScheme(cs);\r
- }\r
- }\r
+ av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ((ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- av.setGlobalColourScheme(cs);\r
- }\r
}\r
\r
/**\r
*/\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
- oldSeq = seq;\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
\r
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
\r
*/\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
- {\r
+ if(wrappedBlock!=startWrapBlock)\r
+ return;\r
+\r
+ if (stretchGroup == null)\r
+ {\r
return;\r
}\r
\r
{\r
res = av.getStartRes();\r
}\r
- else if (res > av.getEndRes())\r
+ else if (res > av.getEndRes() && !av.getWrapAlignment())\r
{\r
res = av.getEndRes();\r
}\r
\r
try\r
{\r
- Thread.sleep(75);\r
+ Thread.sleep(20);\r
}\r
catch (Exception ex)\r
{\r
git://source.jalview.org / jalview.git / blobdiff