import java.awt.*;\r
import java.awt.event.*;\r
\r
-import java.util.*;\r
-\r
import javax.swing.*;\r
\r
\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class SeqPanel extends JPanel\r
+public class SeqPanel extends JPanel implements MouseListener,\r
+ MouseMotionListener, MouseWheelListener\r
+\r
{\r
/** DOCUMENT ME!! */\r
public SeqCanvas seqCanvas;\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
ScrollThread scrollThread = null;\r
boolean mouseDragging = false;\r
boolean editingSeqs = false;\r
\r
ap = p;\r
\r
-\r
- addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- doMouseMoved(evt);\r
- if (editingSeqs)\r
- {\r
- // This is because MacOSX creates a mouseMoved\r
- // If control is down\r
- if(!av.isDataset())\r
- doMouseDragged(evt);\r
- }\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\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
- 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
+ if(!av.isDataset())\r
+ {\r
+ addMouseMotionListener(this);\r
+ addMouseListener(this);\r
+ addMouseWheelListener(this);\r
+ }\r
}\r
\r
int startWrapBlock=-1;\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
+ }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @param evt DOCUMENT ME!\r
*/\r
- public void doMouseReleased(MouseEvent evt)\r
+ public void mouseReleased(MouseEvent evt)\r
{\r
- if (seqEditOccurred > -1)\r
+ mouseDragging = false;\r
+\r
+ if (!editingSeqs)\r
+ {\r
+ doMouseReleasedDefineMode(evt);\r
+ return;\r
+ }\r
+\r
+ if (seqEditOccurred)\r
{\r
- editOccurred(seqEditOccurred);\r
+ editOccurred();\r
}\r
\r
- startseq = -1;\r
- lastres = -1;\r
- seqEditOccurred = -1;\r
- editingSeqs = false;\r
- groupEditing = false;\r
-\r
+ endEditing();\r
ap.repaint();\r
}\r
\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @param evt DOCUMENT ME!\r
*/\r
- public void doMousePressed(MouseEvent evt)\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
+ editingSeqs = true;\r
+ }\r
+ else\r
+ {\r
+ doMousePressedDefineMode(evt);\r
+ return;\r
+ }\r
+\r
+\r
ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",\r
av.alignment, HistoryItem.EDIT));\r
\r
*\r
* @param evt DOCUMENT ME!\r
*/\r
- public void doMouseMoved(MouseEvent evt)\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
* @param evt DOCUMENT ME!\r
*/\r
- public void doMouseDragged(MouseEvent evt)\r
+ public void mouseDragged(MouseEvent evt)\r
{\r
- // If we're dragging we're editing\r
+ if (!editingSeqs)\r
+ {\r
+ doMouseDraggedDefineMode(evt);\r
+ return;\r
+ }\r
+\r
int res = findRes(evt);\r
\r
if (res < 0)\r
{\r
dragRight = false;\r
}\r
+ else if(av.hasHiddenColumns)\r
+ {\r
+ //Stop editing if the user has dragged beyond hiddenBoundary\r
+ int lastCol = av.getColumnSelection().getHiddenRegionBoundary(lastres);\r
+ if( lastCol < res)\r
+ {\r
+ if(lastres!=lastCol)\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
if (res != lastres)\r
{\r
+ SequenceI seq;\r
// Group editing\r
if (groupEditing)\r
{\r
SequenceGroup sg = av.getSelectionGroup();\r
\r
- if (sg == null)\r
+ if (av.hasHiddenRows)\r
{\r
- lastres = -1;\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
+\r
+ if (sg == null)\r
+ {\r
+ endEditing();\r
return;\r
}\r
\r
+ int blankColumn = -1;\r
+\r
// drag to right\r
if (dragRight)\r
{\r
- sg.setEndRes(sg.getEndRes() + (res - lastres));\r
+\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(res-lastres > 1)\r
+ {\r
+ res = lastres+1;\r
+ }\r
+\r
+\r
+ int lastCol = av.getColumnSelection().\r
+ getHiddenRegionBoundary(res);\r
+\r
+ if(lastCol!=res)\r
+ {\r
+ for (blankColumn = lastCol;\r
+ blankColumn > lastres;\r
+ blankColumn--)\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() <= blankColumn)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!jalview.util.Comparison.isGap(\r
+ seq.getSequence().charAt(blankColumn)))\r
+ {\r
+ blank = false;\r
+ continue;\r
+ }\r
+ }\r
+ if (blank)\r
+ break;\r
+ }\r
+\r
+\r
+ if (blankColumn <= lastres)\r
+ {\r
+ endEditing();\r
+ return;\r
+ }\r
+ }\r
+ else\r
+ blankColumn = -1;\r
+\r
+ }\r
+\r
+ sg.setEndRes(sg.getEndRes() + (res - lastres));\r
}\r
\r
// drag to left\r
{\r
/// Are we able to delete?\r
// ie are all columns blank?\r
- boolean deleteAllowed = false;\r
\r
for (int s = 0; s < sg.getSize(); s++)\r
{\r
- SequenceI seq = sg.getSequenceAt(s);\r
+ seq = sg.getSequenceAt(s);\r
\r
for (int j = res; j < lastres; j++)\r
{\r
seq.getSequence().charAt(j)))\r
{\r
// Not a gap, block edit not valid\r
- res = j + 1;\r
- deleteAllowed = false;\r
-\r
- continue;\r
+ endEditing();\r
+ return;\r
}\r
-\r
- deleteAllowed = true;\r
}\r
}\r
\r
- if (!deleteAllowed)\r
+ if(res<sg.getStartRes())\r
{\r
- lastres = -1;\r
-\r
- return;\r
+ sg.setStartRes(sg.getStartRes() - 1);\r
}\r
-\r
sg.setEndRes(sg.getEndRes() - (lastres - res));\r
}\r
\r
for (int i = 0; i < sg.getSize(); i++)\r
{\r
- SequenceI s = sg.getSequenceAt(i);\r
- int k = av.alignment.findIndex(s);\r
+ seq = sg.getSequenceAt(i);\r
\r
// drag to right\r
if (dragRight)\r
{\r
for (int j = lastres; j < res; j++)\r
{\r
- insertChar(j, k);\r
+ insertChar(j, seq, blankColumn);\r
}\r
}\r
\r
{\r
for (int j = res; j < lastres; j++)\r
{\r
- if (s.getLength() > j)\r
+ if (seq.getLength()-1 > res)\r
{\r
- deleteChar(res, k);\r
+ deleteChar(res, seq);\r
}\r
}\r
}\r
}\r
else /////Editing a single sequence///////////\r
{\r
+ seq = av.alignment.getSequenceAt(startseq);\r
if ((res < av.getAlignment().getWidth()) && (res > lastres))\r
{\r
// dragging to the right\r
for (int j = lastres; j < res; j++)\r
{\r
- insertChar(j, startseq);\r
+ insertChar(j, seq, j);\r
}\r
}\r
else if ((res < av.getAlignment().getWidth()) &&\r
av.alignment.getSequenceAt(startseq)\r
.getSequence().charAt(res)))\r
{\r
- deleteChar(res, startseq);\r
+ deleteChar(res, seq);\r
}\r
else\r
{\r
}\r
}\r
\r
+ mouseDragging = true;\r
+ if(scrollThread!=null)\r
+ scrollThread.setEvent(evt);\r
+\r
endEdit = res;\r
lastres = res;\r
seqCanvas.repaint();\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
+\r
+ public void mouseWheelMoved(MouseWheelEvent e)\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
* DOCUMENT ME!\r
* @param j DOCUMENT ME!\r
* @param seq DOCUMENT ME!\r
*/\r
- public void insertChar(int j, int seq)\r
+ void insertChar(int j, SequenceI seq, int blankColumn)\r
{\r
- av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred = seq;\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ //Find the next gap before the end of the visible region boundary\r
+ int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);\r
+ if(lastCol != j)\r
+ {\r
+ if (!groupEditing || lastCol <= j)\r
+ {\r
+ blankColumn = lastCol;\r
+ //If lastCol > j, theres a boundary after the gap insertion\r
+ if (lastCol > j)\r
+ {\r
+ for (blankColumn = lastCol; 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
+\r
+ }\r
+\r
+ // Editing with hidden regions only!!\r
+ seq.deleteCharAt(blankColumn);\r
+ }\r
+ }\r
+\r
+ seq.insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred = true;\r
}\r
\r
/**\r
* @param j DOCUMENT ME!\r
* @param seq DOCUMENT ME!\r
*/\r
- public void deleteChar(int j, int seq)\r
+ public void deleteChar(int j, SequenceI seq)\r
{\r
- av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
- seqEditOccurred = seq;\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ //Find the next gap before the end of the visible region boundary\r
+ int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j);\r
+\r
+ //If lastCol > j, theres a boundary after the gap insertion\r
+ if (lastCol > j)\r
+ {\r
+ seq.insertCharAt(lastCol, av.getGapCharacter());\r
+ }\r
+ }\r
+\r
+ seq.deleteCharAt(j);\r
+ seqEditOccurred = true;\r
\r
- av.alignment.getWidth();\r
seqCanvas.repaint();\r
}\r
\r
*\r
* @param i DOCUMENT ME!\r
*/\r
- void editOccurred(int i)\r
+ void editOccurred()\r
{\r
if (endEdit == startEdit)\r
{\r
*/\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
- if (mouseDragging)\r
- {\r
- stretchGroup.recalcConservation();\r
- mouseDragging = false;\r
- }\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
SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
stretchGroup.getName());\r
+ stretchGroup.recalcConservation();\r
}\r
else\r
{\r
if(wrappedBlock!=startWrapBlock)\r
return;\r
\r
- if (stretchGroup == null)\r
- {\r
+ if (stretchGroup == null)\r
+ {\r
return;\r
- }\r
+ }\r
+\r
\r
- if (res > av.alignment.getWidth())\r
+ if(y > av.alignment.getHeight())\r
{\r
- res = av.alignment.getWidth() - 1;\r
+ y = av.alignment.getHeight() -1;\r
}\r
\r
if (stretchGroup.getEndRes() == res)\r
{\r
res = av.getStartRes();\r
}\r
- else if (res > av.getEndRes() && !av.getWrapAlignment())\r
- {\r
- res = av.getEndRes();\r
- }\r
\r
if (changeEndRes)\r
{\r
dragDirection = -1;\r
}\r
\r
- while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))\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
\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
}\r
\r
- oldSeq = y;\r
+ if(oldSeq < 0)\r
+ oldSeq = -1;\r
+\r
mouseDragging = true;\r
\r
if (scrollThread != null)\r
seqCanvas.repaint();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void doMouseEnteredDefineMode(MouseEvent e)\r
- {\r
- if (scrollThread != null)\r
- {\r
- scrollThread.running = false;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void doMouseExitedDefineMode(MouseEvent e)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
\r
- if (mouseDragging)\r
- {\r
- scrollThread = new ScrollThread();\r
- }\r
- }\r
\r
// this class allows scrolling off the bottom of the visible alignment\r
class ScrollThread extends Thread\r
git://source.jalview.org / jalview.git / commitdiff