import jalview.datamodel.*;\r
import jalview.schemes.*;\r
\r
+import java.util.Vector;\r
+\r
public class SeqPanel\r
extends Panel implements MouseMotionListener, MouseListener\r
{\r
StringBuffer keyboardNo1;\r
StringBuffer keyboardNo2;\r
\r
+ boolean mouseWheelPressed = false;\r
+ Point lastMousePress;\r
+\r
public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
{\r
this.av = avp;\r
\r
\r
endEditing();\r
- while (seqCanvas.cursorY < av.startSeq)\r
- {\r
- ap.scrollUp(true);\r
- }\r
- while (seqCanvas.cursorY + 1 > av.endSeq)\r
+ if (av.wrapAlignment)\r
{\r
- ap.scrollUp(false);\r
+ ap.scrollToWrappedVisible(seqCanvas.cursorX);\r
}\r
- while (seqCanvas.cursorX < av.startRes)\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
+ if (!ap.scrollRight(false))\r
+ break;\r
+ }\r
+ while (seqCanvas.cursorX > av.endRes)\r
+ {\r
+ if (!ap.scrollRight(true))\r
+ break;\r
+ }\r
}\r
-\r
setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),\r
seqCanvas.cursorX, seqCanvas.cursorY);\r
\r
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
+ for(int i=0; i<sg.getSize(false); i++)\r
{\r
int index = av.alignment.findIndex( sg.getSequenceAt(i) );\r
if(index > max)\r
else\r
{\r
// Now add any sequences between min and max\r
- sg.sequences.removeAllElements();\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
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
+ }\r
+\r
if (evt.isShiftDown() || evt.isAltDown() ||\r
evt.isControlDown())\r
{\r
public void mouseReleased(MouseEvent evt)\r
{\r
mouseDragging = false;\r
+ mouseWheelPressed = false;\r
\r
if (!editingSeqs)\r
{\r
editOccurred();\r
\r
endEditing();\r
- ap.repaint();\r
+ ap.repaint();\r
}\r
\r
int startWrapBlock=-1;\r
&& sequence.getSequenceFeatures()!=null\r
&& av.featuresDisplayed!=null)\r
{\r
+ StringBuffer featureText = new StringBuffer();\r
+ Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));\r
+\r
int index = 0;\r
- sequence.getSequenceFeatures();\r
- boolean first = true;\r
- while (index < sequence.getSequenceFeatures().length)\r
+ while (index < allFeatures.size())\r
{\r
- SequenceFeature sf = sequence.getSequenceFeatures()[index];\r
- if (sf.getBegin() <= sequence.findPosition(res) &&\r
- sf.getEnd() >= sequence.findPosition(res))\r
- {\r
- if(!av.featuresDisplayed.containsKey(sf.getType()))\r
- {\r
- index++;\r
- continue;\r
- }\r
-\r
- if(first)\r
- {\r
- text.append(" Sequence Feature:");\r
- first = false;\r
- }\r
+ SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);\r
\r
- text.append(" "+sf.getType());\r
+ featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);\r
\r
- if(sf.getDescription()!=null)\r
- text.append(" "+sf.getDescription());\r
+ if (sf.getDescription() != null)\r
+ featureText.append(" " + sf.getDescription());\r
\r
- if (sf.getStatus()!=null && sf.getStatus().length() > 0)\r
- {\r
- text.append(" (" + sf.getStatus() + ")");\r
- }\r
- text.append("; ");\r
+ if (sf.getValue("status") != null )\r
+ {\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
+ // text.append(" Sequence Feature:");\r
+ // text.append(featureText);\r
+\r
}\r
\r
+\r
ap.alignFrame.statusBar.setText(text.toString());\r
\r
}\r
\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
+ Tooltip tooltip;\r
+\r
public void mouseDragged(MouseEvent evt)\r
{\r
- if (!editingSeqs)\r
-{\r
- doMouseDraggedDefineMode(evt);\r
- return;\r
-}\r
+ if (mouseWheelPressed)\r
+ {\r
+ int oldWidth = av.charWidth;\r
+\r
+ //Which is bigger, left-right or up-down?\r
+ if (Math.abs(evt.getY() - lastMousePress.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
+\r
+ if(fontSize<1)\r
+ fontSize = 1;\r
+\r
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));\r
+ av.charWidth = oldWidth;\r
+ }\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
+ 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
\r
//Are we editing within a selection group?\r
if (groupEditing\r
- || (sg != null && sg.sequences.contains(seq)))\r
+ || (sg != null && sg.getSequences(false).contains(seq)))\r
{\r
fixedColumns = true;\r
\r
fixedRight--)\r
{\r
blank = true;\r
- for (int s = 0; s < sg.getSize(); s++)\r
+ for (int s = 0; s < sg.getSize(false); s++)\r
{\r
seq = sg.getSequenceAt(s);\r
for (int j = 0; j < startres - lastres; j++)\r
\r
if (!blank)\r
{\r
- if(sg.getSize() == av.alignment.getHeight())\r
+ if(sg.getSize(false) == av.alignment.getHeight())\r
{\r
//We can still insert gaps if the selectionGroup\r
//contains all the sequences\r
/// Are we able to delete?\r
// ie are all columns blank?\r
\r
- for (int s = 0; s < sg.getSize(); s++)\r
+ for (int s = 0; s < sg.getSize(false); s++)\r
{\r
seq = sg.getSequenceAt(s);\r
\r
}\r
\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
seq = sg.getSequenceAt(i);\r
\r
//////////////////////////////////////////\r
public void doMousePressedDefineMode(MouseEvent evt)\r
{\r
+\r
+\r
if (scrollThread != null)\r
{\r
scrollThread.running = false;\r
}\r
}\r
\r
- else if (!stretchGroup.sequences.contains(sequence)\r
+ else if (!stretchGroup.getSequences(false).contains(sequence)\r
|| stretchGroup.getStartRes() > res\r
|| stretchGroup.getEndRes() < res)\r
{\r
allGroups[i].getEndRes() >= res)\r
{\r
stretchGroup = allGroups[i];\r
- av.setSelectionGroup(stretchGroup);\r
break;\r
}\r
}\r
}\r
+ av.setSelectionGroup(stretchGroup);\r
}\r
\r
- if (stretchGroup == null)\r
+ if (av.cursorMode)\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
+ seqCanvas.cursorX = findRes(evt);\r
+ seqCanvas.cursorY = findSeq(evt);\r
+ seqCanvas.repaint();\r
+ return;\r
}\r
\r
+\r
+\r
// DETECT RIGHT MOUSE BUTTON IN AWT\r
- else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
+ if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
InputEvent.BUTTON3_MASK)\r
{\r
- APopupMenu popup = new APopupMenu(ap, null, 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
}\r
-\r
- if (stretchGroup != null && stretchGroup.getEndRes() == res)\r
+ else\r
{\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
- }\r
+ //Only if left mouse button do we want to change group sizes\r
\r
- else if (stretchGroup != null && stretchGroup.getStartRes() == res)\r
- {\r
- // Edit end res position of selected group\r
- changeStartRes = true;\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, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
+ if (av.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
+ "Background");\r
+ }\r
\r
+ }\r
+\r
+ if (stretchGroup != null && stretchGroup.getEndRes() == res)\r
+ {\r
+ // Edit end res position of selected group\r
+ changeEndRes = true;\r
+ }\r
+\r
+ else if (stretchGroup != null && stretchGroup.getStartRes() == res)\r
+ {\r
+ // Edit end res position of selected group\r
+ changeStartRes = true;\r
+ }\r
+ }\r
}\r
\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
if (stretchGroup.cs instanceof ClustalxColourScheme)\r
{\r
- ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
- sequences,\r
+ ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
+ stretchGroup.getSequences(true),\r
stretchGroup.getWidth());\r
}\r
\r
\r
Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
\r
- if (stretchGroup.sequences.contains(nextSeq))\r
+ if (stretchGroup.getSequences(false).contains(nextSeq))\r
{\r
stretchGroup.deleteSequence(seq, false);\r
}\r
git://source.jalview.org / jalview.git / blobdiff