X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=unused%2Fappletgui%2FIdPanel.java;fp=unused%2Fappletgui%2FIdPanel.java;h=9292749809d1b4f4336ed4d7b7b9d9f15e987268;hb=6319110ce33faa76ee6cf9832e78faa224510fed;hp=c4b9651aaf1a45caefcb30ce10bdffc4c4f5396f;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44;p=jalviewjs.git
diff --git a/unused/appletgui/IdPanel.java b/unused/appletgui/IdPanel.java
index c4b9651..9292749 100644
--- a/unused/appletgui/IdPanel.java
+++ b/unused/appletgui/IdPanel.java
@@ -1,498 +1,498 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see .
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.UrlLink;
-import jalview.viewmodel.AlignmentViewport;
-
-import java.awt.BorderLayout;
-import java.awt.Panel;
-import java.awt.event.InputEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.util.List;
-import java.util.Vector;
-
-public class IdPanel extends Panel implements MouseListener,
- MouseMotionListener
-{
-
- protected IdCanvas idCanvas;
-
- protected AlignmentViewport av;
-
- protected AlignmentPanel alignPanel;
-
- ScrollThread scrollThread = null;
-
- int lastid = -1;
-
- boolean mouseDragging = false;
-
- java.util.Vector links = new java.util.Vector();
-
- public IdPanel(AlignViewport av, AlignmentPanel parent)
- {
- this.av = av;
- alignPanel = parent;
- idCanvas = new IdCanvas(av);
- setLayout(new BorderLayout());
- add(idCanvas, BorderLayout.CENTER);
- idCanvas.addMouseListener(this);
- idCanvas.addMouseMotionListener(this);
-
- String label, url;
- // TODO: add in group link parameter
- if (av.applet != null)
- {
- for (int i = 1; i < 10; i++)
- {
- label = av.applet.getParameter("linkLabel_" + i);
- url = av.applet.getParameter("linkURL_" + i);
-
- if (label != null && url != null)
- {
- links.addElement(label + "|" + url);
- }
-
- }
- }
- {
- // upgrade old SRS link
- int srsPos = links
- .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
- if (srsPos > -1)
- {
- links.setElementAt(
- "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
- srsPos);
- }
- }
- if (links.size() < 1)
- {
- links = new java.util.Vector();
- links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
- }
- }
-
- Tooltip tooltip;
-
- public void mouseMoved(MouseEvent e)
- {
- int seq = alignPanel.seqPanel.findSeq(e);
-
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-
- // look for non-pos features
- StringBuffer tooltiptext = new StringBuffer();
- if (sequence != null)
- {
- if (sequence.getDescription() != null)
- {
- tooltiptext.append(sequence.getDescription());
- tooltiptext.append("\n");
- }
-
- SequenceFeature sf[] = sequence.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
- {
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
- {
- boolean nl = false;
- if (sf[sl].getFeatureGroup() != null)
- {
- tooltiptext.append(sf[sl].getFeatureGroup());
- nl = true;
- }
- ;
- if (sf[sl].getType() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getType());
- nl = true;
- }
- ;
- if (sf[sl].getDescription() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getDescription());
- nl = true;
- }
- ;
- if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
- {
- tooltiptext.append(" Score = ");
- tooltiptext.append(sf[sl].getScore());
- nl = true;
- }
- ;
- if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
- {
- tooltiptext.append(" (");
- tooltiptext.append(sf[sl].getStatus());
- tooltiptext.append(")");
- nl = true;
- }
- ;
- if (nl)
- {
- tooltiptext.append("\n");
- }
- }
- }
- }
- if (tooltiptext.length() == 0)
- {
- // nothing to display - so clear tooltip if one is visible
- if (tooltip != null)
- {
- tooltip.setVisible(false);
- }
- tooltip = null;
- tooltiptext = null;
- return;
- }
- if (tooltip == null)
- {
- tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
- + tooltiptext.toString(), idCanvas);
- }
- else
- {
- tooltip.setTip(sequence.getDisplayId(true) + "\n"
- + tooltiptext.toString());
- }
- tooltiptext = null;
- }
-
- public void mouseDragged(MouseEvent e)
- {
- mouseDragging = true;
-
- int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
-
- if (seq < lastid)
- {
- selectSeqs(lastid - 1, seq);
- }
- else if (seq > lastid)
- {
- selectSeqs(lastid + 1, seq);
- }
-
- lastid = seq;
- alignPanel.paintAlignment(false);
- }
-
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() < 2)
- {
- return;
- }
-
- // DEFAULT LINK IS FIRST IN THE LINK LIST
- int seq = alignPanel.seqPanel.findSeq(e);
- SequenceI sq = av.getAlignment().getSequenceAt(seq);
- if (sq == null)
- {
- return;
- }
- String id = sq.getName();
-
- String target = null;
- String url = null;
- int i = 0;
- while (url == null && i < links.size())
- {
- // DEFAULT LINK IS FIRST IN THE LINK LIST
- // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
- url = links.elementAt(i++).toString();
- UrlLink urlLink = null;
- try
- {
- urlLink = new UrlLink(url);
- target = urlLink.getTarget();
- } catch (Exception foo)
- {
- System.err.println("Exception for URLLink '" + url + "'");
- foo.printStackTrace();
- url = null;
- continue;
- }
- ;
- if (!urlLink.isValid())
- {
- System.err.println(urlLink.getInvalidMessage());
- url = null;
- continue;
- }
-
- String urls[] = urlLink.makeUrls(id, true);
- if (urls == null || urls[0] == null || urls[0].length() < 1)
- {
- url = null;
- continue;
- }
- // just take first URL made from regex
- url = urls[1];
- }
- try
- {
-
- alignPanel.alignFrame.showURL(url, target);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- public void mouseEntered(MouseEvent e)
- {
- if (scrollThread != null)
- {
- scrollThread.running = false;
- }
- }
-
- public void mouseExited(MouseEvent e)
- {
- if (av.getWrapAlignment())
- {
- return;
- }
-
- if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
- {
- scrollThread = new ScrollThread(true);
- }
-
- if (mouseDragging && e.getY() >= getSize().height
- && av.getAlignment().getHeight() > av.getEndSeq())
- {
- scrollThread = new ScrollThread(false);
- }
- }
-
- public void mousePressed(MouseEvent e)
- {
- if (e.getClickCount() > 1)
- {
- return;
- }
-
- int y = e.getY();
- if (av.getWrapAlignment())
- {
- y -= 2 * av.getCharHeight();
- }
-
- int seq = alignPanel.seqPanel.findSeq(e);
-
- if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
- {
- Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
-
- // build a new links menu based on the current links + any non-positional
- // features
- Vector nlinks = new Vector();
- for (int l = 0, lSize = links.size(); l < lSize; l++)
- {
- nlinks.addElement(links.elementAt(l));
- }
- SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
- {
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
- {
- if (sf[sl].links != null && sf[sl].links.size() > 0)
- {
- for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
- {
- nlinks.addElement(sf[sl].links.elementAt(l));
- }
- }
- }
- }
-
- APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
- this.add(popup);
- popup.show(this, e.getX(), e.getY());
- return;
- }
-
- if ((av.getSelectionGroup() == null)
- || ((!e.isControlDown() && !e.isShiftDown()) && av
- .getSelectionGroup() != null))
- {
- av.setSelectionGroup(new SequenceGroup());
- av.getSelectionGroup().setStartRes(0);
- av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
- }
-
- if (e.isShiftDown() && lastid != -1)
- {
- selectSeqs(lastid, seq);
- }
- else
- {
- selectSeq(seq);
- }
-
- alignPanel.paintAlignment(false);
- }
-
- void selectSeq(int seq)
- {
- lastid = seq;
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, true);
- }
-
- void selectSeqs(int start, int end)
- {
-
- lastid = start;
-
- if (end >= av.getAlignment().getHeight())
- {
- end = av.getAlignment().getHeight() - 1;
- }
-
- if (end < start)
- {
- int tmp = start;
- start = end;
- end = tmp;
- lastid = end;
- }
- if (av.getSelectionGroup() == null)
- {
- av.setSelectionGroup(new SequenceGroup());
- }
- for (int i = start; i <= end; i++)
- {
- av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), i == end);
- }
-
- }
-
- public void mouseReleased(MouseEvent e)
- {
- if (scrollThread != null)
- {
- scrollThread.running = false;
- }
-
- if (av.getSelectionGroup() != null)
- {
- av.getSelectionGroup().recalcConservation();
- }
-
- mouseDragging = false;
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- // always send selection message when mouse is released
- av.sendSelection();
- }
-
- public void highlightSearchResults(List list)
- {
- idCanvas.setHighlighted(list);
-
- if (list == null)
- {
- return;
- }
-
- int index = av.getAlignment().findIndex(list.get(0));
-
- // do we need to scroll the panel?
- if (av.getStartSeq() > index || av.getEndSeq() < index)
- {
- alignPanel.setScrollValues(av.getStartRes(), index);
- }
- }
-
- // this class allows scrolling off the bottom of the visible alignment
- class ScrollThread extends Thread
- {
- boolean running = false;
-
- boolean up = true;
-
- public ScrollThread(boolean up)
- {
- this.up = up;
- start();
- }
-
- public void stopScrolling()
- {
- running = false;
- }
-
- public void run()
- {
- running = true;
- while (running)
- {
- if (alignPanel.scrollUp(up))
- {
- // scroll was ok, so add new sequence to selection
- int seq = av.getStartSeq();
- if (!up)
- {
- seq = av.getEndSeq();
- }
-
- if (seq < lastid)
- {
- selectSeqs(lastid - 1, seq);
- }
- else if (seq > lastid && seq < av.getAlignment().getHeight())
- {
- selectSeqs(lastid + 1, seq);
- }
-
- lastid = seq;
- }
- else
- {
- running = false;
- }
-
- alignPanel.paintAlignment(true);
- try
- {
- Thread.sleep(100);
- } catch (Exception ex)
- {
- }
- }
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Panel;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.List;
+import java.util.Vector;
+
+public class IdPanel extends Panel implements MouseListener,
+ MouseMotionListener
+{
+
+ protected IdCanvas idCanvas;
+
+ protected AlignmentViewport av;
+
+ protected AlignmentPanel alignPanel;
+
+ ScrollThread scrollThread = null;
+
+ int lastid = -1;
+
+ boolean mouseDragging = false;
+
+ java.util.Vector links = new java.util.Vector();
+
+ public IdPanel(AlignViewport av, AlignmentPanel parent)
+ {
+ this.av = av;
+ alignPanel = parent;
+ idCanvas = new IdCanvas(av);
+ setLayout(new BorderLayout());
+ add(idCanvas, BorderLayout.CENTER);
+ idCanvas.addMouseListener(this);
+ idCanvas.addMouseMotionListener(this);
+
+ String label, url;
+ // TODO: add in group link parameter
+ if (av.applet != null)
+ {
+ for (int i = 1; i < 10; i++)
+ {
+ label = av.applet.getParameter("linkLabel_" + i);
+ url = av.applet.getParameter("linkURL_" + i);
+
+ if (label != null && url != null)
+ {
+ links.addElement(label + "|" + url);
+ }
+
+ }
+ }
+ {
+ // upgrade old SRS link
+ int srsPos = links
+ .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ if (srsPos > -1)
+ {
+ links.setElementAt(
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+ srsPos);
+ }
+ }
+ if (links.size() < 1)
+ {
+ links = new java.util.Vector();
+ links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+ }
+ }
+
+ Tooltip tooltip;
+
+ public void mouseMoved(MouseEvent e)
+ {
+ int seq = alignPanel.seqPanel.findSeq(e);
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+ // look for non-pos features
+ StringBuffer tooltiptext = new StringBuffer();
+ if (sequence != null)
+ {
+ if (sequence.getDescription() != null)
+ {
+ tooltiptext.append(sequence.getDescription());
+ tooltiptext.append("\n");
+ }
+
+ SequenceFeature sf[] = sequence.getSequenceFeatures();
+ for (int sl = 0; sf != null && sl < sf.length; sl++)
+ {
+ if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ {
+ boolean nl = false;
+ if (sf[sl].getFeatureGroup() != null)
+ {
+ tooltiptext.append(sf[sl].getFeatureGroup());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getType() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf[sl].getType());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getDescription() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf[sl].getDescription());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f)
+ {
+ tooltiptext.append(" Score = ");
+ tooltiptext.append(sf[sl].getScore());
+ nl = true;
+ }
+ ;
+ if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
+ {
+ tooltiptext.append(" (");
+ tooltiptext.append(sf[sl].getStatus());
+ tooltiptext.append(")");
+ nl = true;
+ }
+ ;
+ if (nl)
+ {
+ tooltiptext.append("\n");
+ }
+ }
+ }
+ }
+ if (tooltiptext.length() == 0)
+ {
+ // nothing to display - so clear tooltip if one is visible
+ if (tooltip != null)
+ {
+ tooltip.setVisible(false);
+ }
+ tooltip = null;
+ tooltiptext = null;
+ return;
+ }
+ if (tooltip == null)
+ {
+ tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
+ + tooltiptext.toString(), idCanvas);
+ }
+ else
+ {
+ tooltip.setTip(sequence.getDisplayId(true) + "\n"
+ + tooltiptext.toString());
+ }
+ tooltiptext = null;
+ }
+
+ public void mouseDragged(MouseEvent e)
+ {
+ mouseDragging = true;
+
+ int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
+ }
+ else if (seq > lastid)
+ {
+ selectSeqs(lastid + 1, seq);
+ }
+
+ lastid = seq;
+ alignPanel.paintAlignment(false);
+ }
+
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() < 2)
+ {
+ return;
+ }
+
+ // DEFAULT LINK IS FIRST IN THE LINK LIST
+ int seq = alignPanel.seqPanel.findSeq(e);
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
+ if (sq == null)
+ {
+ return;
+ }
+ String id = sq.getName();
+
+ String target = null;
+ String url = null;
+ int i = 0;
+ while (url == null && i < links.size())
+ {
+ // DEFAULT LINK IS FIRST IN THE LINK LIST
+ // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
+ url = links.elementAt(i++).toString();
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(url);
+ target = urlLink.getTarget();
+ } catch (Exception foo)
+ {
+ System.err.println("Exception for URLLink '" + url + "'");
+ foo.printStackTrace();
+ url = null;
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ System.err.println(urlLink.getInvalidMessage());
+ url = null;
+ continue;
+ }
+
+ String urls[] = urlLink.makeUrls(id, true);
+ if (urls == null || urls[0] == null || urls[0].length() < 1)
+ {
+ url = null;
+ continue;
+ }
+ // just take first URL made from regex
+ url = urls[1];
+ }
+ try
+ {
+
+ alignPanel.alignFrame.showURL(url, target);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ public void mouseEntered(MouseEvent e)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
+ }
+
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
+ {
+ scrollThread = new ScrollThread(true);
+ }
+
+ if (mouseDragging && e.getY() >= getSize().height
+ && av.getAlignment().getHeight() > av.getEndSeq())
+ {
+ scrollThread = new ScrollThread(false);
+ }
+ }
+
+ public void mousePressed(MouseEvent e)
+ {
+ if (e.getClickCount() > 1)
+ {
+ return;
+ }
+
+ int y = e.getY();
+ if (av.getWrapAlignment())
+ {
+ y -= 2 * av.getCharHeight();
+ }
+
+ int seq = alignPanel.seqPanel.findSeq(e);
+
+ if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+ Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+
+ // build a new links menu based on the current links + any non-positional
+ // features
+ Vector nlinks = new Vector();
+ for (int l = 0, lSize = links.size(); l < lSize; l++)
+ {
+ nlinks.addElement(links.elementAt(l));
+ }
+ SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
+ for (int sl = 0; sf != null && sl < sf.length; sl++)
+ {
+ if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ {
+ if (sf[sl].links != null && sf[sl].links.size() > 0)
+ {
+ for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
+ {
+ nlinks.addElement(sf[sl].links.elementAt(l));
+ }
+ }
+ }
+ }
+
+ APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
+ this.add(popup);
+ popup.show(this, e.getX(), e.getY());
+ return;
+ }
+
+ if ((av.getSelectionGroup() == null)
+ || ((!e.isControlDown() && !e.isShiftDown()) && av
+ .getSelectionGroup() != null))
+ {
+ av.setSelectionGroup(new SequenceGroup());
+ av.getSelectionGroup().setStartRes(0);
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
+ }
+
+ if (e.isShiftDown() && lastid != -1)
+ {
+ selectSeqs(lastid, seq);
+ }
+ else
+ {
+ selectSeq(seq);
+ }
+
+ alignPanel.paintAlignment(false);
+ }
+
+ void selectSeq(int seq)
+ {
+ lastid = seq;
+ SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+ av.getSelectionGroup().addOrRemove(pickedSeq, true);
+ }
+
+ void selectSeqs(int start, int end)
+ {
+
+ lastid = start;
+
+ if (end >= av.getAlignment().getHeight())
+ {
+ end = av.getAlignment().getHeight() - 1;
+ }
+
+ if (end < start)
+ {
+ int tmp = start;
+ start = end;
+ end = tmp;
+ lastid = end;
+ }
+ if (av.getSelectionGroup() == null)
+ {
+ av.setSelectionGroup(new SequenceGroup());
+ }
+ for (int i = start; i <= end; i++)
+ {
+ av.getSelectionGroup().addSequence(
+ av.getAlignment().getSequenceAt(i), i == end);
+ }
+
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ }
+
+ if (av.getSelectionGroup() != null)
+ {
+ av.getSelectionGroup().recalcConservation();
+ }
+
+ mouseDragging = false;
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // always send selection message when mouse is released
+ av.sendSelection();
+ }
+
+ public void highlightSearchResults(List list)
+ {
+ idCanvas.setHighlighted(list);
+
+ if (list == null)
+ {
+ return;
+ }
+
+ int index = av.getAlignment().findIndex(list.get(0));
+
+ // do we need to scroll the panel?
+ if (av.getStartSeq() > index || av.getEndSeq() < index)
+ {
+ alignPanel.setScrollValues(av.getStartRes(), index);
+ }
+ }
+
+ // this class allows scrolling off the bottom of the visible alignment
+ class ScrollThread extends Thread
+ {
+ boolean running = false;
+
+ boolean up = true;
+
+ public ScrollThread(boolean up)
+ {
+ this.up = up;
+ start();
+ }
+
+ public void stopScrolling()
+ {
+ running = false;
+ }
+
+ public void run()
+ {
+ running = true;
+ while (running)
+ {
+ if (alignPanel.scrollUp(up))
+ {
+ // scroll was ok, so add new sequence to selection
+ int seq = av.getStartSeq();
+ if (!up)
+ {
+ seq = av.getEndSeq();
+ }
+
+ if (seq < lastid)
+ {
+ selectSeqs(lastid - 1, seq);
+ }
+ else if (seq > lastid && seq < av.getAlignment().getHeight())
+ {
+ selectSeqs(lastid + 1, seq);
+ }
+
+ lastid = seq;
+ }
+ else
+ {
+ running = false;
+ }
+
+ alignPanel.paintAlignment(true);
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
+}