/*\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) 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
\r
package jalview.appletgui;\r
\r
\r
import jalview.datamodel.*;\r
\r
-public class IdPanel extends Panel implements MouseListener, MouseMotionListener {\r
+public class IdPanel\r
+ extends Panel implements MouseListener, MouseMotionListener\r
+{\r
\r
- protected IdCanvas idCanvas;\r
- protected AlignViewport av;\r
+ protected IdCanvas idCanvas;\r
+ protected AlignViewport av;\r
protected AlignmentPanel alignPanel;\r
ScrollThread scrollThread = null;\r
\r
- int offy;\r
- int width;\r
+ int offy;\r
+ int width;\r
int lastid = -1;\r
boolean mouseDragging = false;\r
+ java.util.Vector links = new java.util.Vector();\r
\r
public IdPanel(AlignViewport av, AlignmentPanel parent)\r
{\r
- this.av = av;\r
+ this.av = av;\r
alignPanel = parent;\r
idCanvas = new IdCanvas(av);\r
setLayout(new BorderLayout());\r
add(idCanvas, BorderLayout.CENTER);\r
idCanvas.addMouseListener(this);\r
idCanvas.addMouseMotionListener(this);\r
- }\r
\r
- public void mouseMoved(MouseEvent e) {}\r
+ String label, url;\r
+ if(parent.alignFrame.applet!=null)\r
+ {\r
+ for (int i = 1; i < 10; i++)\r
+ {\r
+ label = parent.alignFrame.applet.getParameter("linkLabel_" + i);\r
+ url = parent.alignFrame.applet.getParameter("linkURL_" + i);\r
+\r
+ if (label != null && url != null)\r
+ links.addElement(label + "|" + url);\r
+\r
+ }\r
+ }\r
+ if (links.size() < 1)\r
+ {\r
+ links = new java.util.Vector();\r
+ links.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");\r
+ }\r
+ }\r
\r
+ public void mouseMoved(MouseEvent e)\r
+ {}\r
\r
- public void mouseDragged(MouseEvent e) {\r
+ public void mouseDragged(MouseEvent e)\r
+ {\r
mouseDragging = true;\r
\r
int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y -= 2 * av.charHeight;\r
+ }\r
int seq = av.getIndex(y);\r
\r
- if(seq<0)\r
+ if (seq < 0)\r
+ {\r
return;\r
+ }\r
\r
if (seq < lastid)\r
+ {\r
selectSeqs(lastid - 1, seq);\r
+ }\r
else if (seq > lastid)\r
+ {\r
selectSeqs(lastid + 1, seq);\r
+ }\r
\r
lastid = seq;\r
alignPanel.repaint();\r
\r
public void mouseClicked(MouseEvent e)\r
{\r
- if (e.getClickCount() == 2)\r
+ if (e.getClickCount() < 2)\r
+ return;\r
+\r
+ int y = e.getY();\r
+\r
+ if (av.getWrapAlignment())\r
{\r
- int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
-\r
- int seq = av.getIndex(y);\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
-\r
- try{\r
- jalview.bin.JalviewLite.showURL(\r
- "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +\r
- "]+-vn+2");\r
- }catch(Exception ex){ex.printStackTrace();}\r
+ y -= (2 * av.charHeight);\r
}\r
\r
+ //DEFAULT LINK IS FIRST IN THE LINK LIST\r
+ int seq = av.getIndex(y);\r
+ String id = av.getAlignment().getSequenceAt(seq).getName();\r
+ if (id.indexOf("|") > -1)\r
+ id = id.substring(id.lastIndexOf("|") + 1);\r
+\r
+ String target = links.elementAt(0).toString();\r
+ target = target.substring(0, target.indexOf("|"));\r
+ String url = links.elementAt(0).toString();\r
+ url = url.substring(url.indexOf("|")+1);\r
+\r
+ int index = url.indexOf("$SEQUENCE_ID$");\r
+ url = url.substring(0, index)+ id + url.substring(index+13);\r
+\r
+ try\r
+ {\r
+\r
+ alignPanel.alignFrame.showURL(url, target);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
+\r
public void mouseEntered(MouseEvent e)\r
{\r
- if(scrollThread!=null)\r
+ if (scrollThread != null)\r
+ {\r
scrollThread.running = false;\r
+ }\r
}\r
\r
- public void mouseExited (MouseEvent e)\r
+ public void mouseExited(MouseEvent e)\r
{\r
- if(av.getWrapAlignment())\r
+ if (av.getWrapAlignment())\r
+ {\r
return;\r
+ }\r
\r
- if(mouseDragging && e.getY()<0 && av.getStartSeq()>0)\r
+ if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)\r
{\r
scrollThread = new ScrollThread(true);\r
}\r
\r
- if(mouseDragging && e.getY()>=getSize().height && av.alignment.getHeight()>av.getEndSeq())\r
+ if (mouseDragging && e.getY() >= getSize().height &&\r
+ av.alignment.getHeight() > av.getEndSeq())\r
{\r
scrollThread = new ScrollThread(false);\r
}\r
}\r
\r
-\r
- public void mousePressed(MouseEvent e) {\r
- if (e.getClickCount() == 2)\r
+ public void mousePressed(MouseEvent e)\r
+ {\r
+ if (e.getClickCount() >1 )\r
+ {\r
return;\r
+ }\r
\r
int y = e.getY();\r
- if(av.getWrapAlignment())\r
- y-=2*av.charHeight;\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y -= 2 * av.charHeight;\r
+ }\r
\r
int seq = av.getIndex(y);\r
if (seq == -1)\r
+ {\r
return;\r
+ }\r
\r
- if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)\r
+ if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
+ InputEvent.BUTTON3_MASK)\r
{\r
- APopupMenu popup = new APopupMenu(alignPanel, null);\r
+ APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links);\r
this.add(popup);\r
popup.show(this, e.getX(), e.getY());\r
return;\r
}\r
\r
-\r
- if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)\r
+ if (!e.isControlDown() && !e.isShiftDown() &&\r
+ av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null)\r
{\r
\r
SequenceGroup selection = new SequenceGroup();\r
SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));\r
selection.setStartRes(0);\r
- selection.setEndRes(av.alignment.getWidth()-1);\r
- for (int i =0; i< sg.getSize(); i++)\r
- selection.addSequence(sg.getSequenceAt(i));\r
+ selection.setEndRes(av.alignment.getWidth() - 1);\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ selection.addSequence(sg.getSequenceAt(i), true);\r
+ }\r
\r
av.setSelectionGroup(selection);\r
return;\r
}\r
\r
- if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))\r
+ if (av.getSelectionGroup() == null ||\r
+ (!e.isControlDown() && av.getSelectionGroup() != null))\r
+ {\r
av.setSelectionGroup(new SequenceGroup());\r
+ }\r
\r
av.getSelectionGroup().setStartRes(0);\r
- av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);\r
+ av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);\r
\r
- if(e.isShiftDown() && lastid!=-1)\r
+ if (e.isShiftDown() && lastid != -1)\r
+ {\r
selectSeqs(lastid, seq);\r
+ }\r
else\r
+ {\r
selectSeq(seq);\r
+ }\r
\r
alignPanel.repaint();\r
}\r
{\r
lastid = seq;\r
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);\r
- av.getSelectionGroup().addOrRemove(pickedSeq);\r
+ av.getSelectionGroup().addOrRemove(pickedSeq, false);\r
}\r
\r
- void selectSeqs(int start, int end) {\r
+ void selectSeqs(int start, int end)\r
+ {\r
\r
lastid = start;\r
if (end < start)\r
- {\r
- int tmp = start;\r
- start = end;\r
- end = tmp;\r
- lastid = end;\r
- }\r
-\r
- for (int i = start; i <= end; i++)\r
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));\r
+ {\r
+ int tmp = start;\r
+ start = end;\r
+ end = tmp;\r
+ lastid = end;\r
+ }\r
\r
- }\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);\r
+ }\r
\r
+ }\r
\r
public void mouseReleased(MouseEvent e)\r
{\r
- if(scrollThread!=null)\r
+ if (scrollThread != null)\r
+ {\r
scrollThread.running = false;\r
+ }\r
+\r
+ if(av.getSelectionGroup()!=null)\r
+ av.getSelectionGroup().recalcConservation();\r
\r
mouseDragging = false;\r
- PaintRefresher.Refresh(this);\r
+ PaintRefresher.Refresh(this, av.alignment);\r
}\r
\r
- public void highlightSearchResults( java.util.Vector found )\r
+ public void highlightSearchResults(java.util.Vector found)\r
{\r
- idCanvas.setHighlighted( found );\r
+ idCanvas.setHighlighted(found);\r
\r
- if(found == null)\r
+ if (found == null)\r
+ {\r
return;\r
+ }\r
\r
- int index = av.alignment.findIndex( (SequenceI)found.elementAt(0));\r
+ int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));\r
\r
// do we need to scroll the panel?\r
- if(av.getStartSeq()>index || av.getEndSeq()<index)\r
- alignPanel.setScrollValues( av.getStartRes(), index);\r
+ if (av.getStartSeq() > index || av.getEndSeq() < index)\r
+ {\r
+ alignPanel.setScrollValues(av.getStartRes(), index);\r
+ }\r
}\r
\r
// this class allows scrolling off the bottom of the visible alignment\r
running = true;\r
while (running)\r
{\r
- if(alignPanel.scrollUp(up))\r
+ if (alignPanel.scrollUp(up))\r
{\r
// scroll was ok, so add new sequence to selection\r
int seq = av.getStartSeq();\r
- if(!up)\r
+ if (!up)\r
+ {\r
seq = av.getEndSeq();\r
+ }\r
\r
if (seq < lastid)\r
+ {\r
selectSeqs(lastid - 1, seq);\r
+ }\r
else if (seq > lastid)\r
+ {\r
selectSeqs(lastid + 1, seq);\r
+ }\r
\r
lastid = seq;\r
}\r
else\r
+ {\r
running = false;\r
+ }\r
\r
alignPanel.repaint();\r
try\r
{}\r
}\r
}\r
-}\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff