X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=af1c47b18626dc67b4e465e2a8f092da85db844a;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=e427f425695ecc06402865a607d2703dd79d0240;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index e427f42..af1c47b 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,58 +1,66 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * 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 java.awt.*;
-import java.awt.event.*;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.applet.AppletUrlProviderFactory;
+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.ArrayList;
+import java.util.HashMap;
import java.util.List;
-import java.util.Vector;
-import jalview.datamodel.*;
-import jalview.util.UrlLink;
-
-public class IdPanel extends Panel implements MouseListener,
- MouseMotionListener
+public class IdPanel extends Panel
+ implements MouseListener, MouseMotionListener
{
protected IdCanvas idCanvas;
- protected AlignViewport av;
+ protected AlignmentViewport av;
protected AlignmentPanel alignPanel;
ScrollThread scrollThread = null;
- int offy;
-
- int width;
-
int lastid = -1;
boolean mouseDragging = false;
- java.util.Vector links = new java.util.Vector();
+ UrlProviderI urlProvider = null;
- public IdPanel(AlignViewport av, AlignmentPanel parent)
+ public IdPanel(AlignViewport viewport, AlignmentPanel parent)
{
- this.av = av;
+ this.av = viewport;
alignPanel = parent;
- idCanvas = new IdCanvas(av);
+ idCanvas = new IdCanvas(viewport);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
idCanvas.addMouseListener(this);
@@ -60,104 +68,94 @@ public class IdPanel extends Panel implements MouseListener,
String label, url;
// TODO: add in group link parameter
- if (av.applet != null)
+
+ // make a list of label,url pairs
+ HashMap urlList = new HashMap<>();
+ if (viewport.applet != null)
{
for (int i = 1; i < 10; i++)
{
- label = av.applet.getParameter("linkLabel_" + i);
- url = av.applet.getParameter("linkURL_" + i);
+ label = viewport.applet.getParameter("linkLabel_" + i);
+ url = viewport.applet.getParameter("linkURL_" + i);
- if (label != null && url != null)
+ // only add non-null parameters
+ if (label != null)
{
- links.addElement(label + "|" + url);
+ urlList.put(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)
+
+ if (!urlList.isEmpty())
{
- links.setElementAt(
- "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
- srsPos);
+ // set default as first entry in list
+ String defaultUrl = viewport.applet.getParameter("linkLabel_1");
+ UrlProviderFactoryI factory = new AppletUrlProviderFactory(
+ defaultUrl, urlList);
+ urlProvider = factory.createUrlProvider();
}
}
- 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;
+ @Override
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 == null)
+ {
+ return;
+ }
+ if (sequence.getDescription() != null)
+ {
+ tooltiptext.append(sequence.getDescription());
+ tooltiptext.append("\n");
+ }
+
+ for (SequenceFeature sf : sequence.getFeatures()
+ .getNonPositionalFeatures())
{
- if (sequence.getDescription() != null)
+ boolean nl = false;
+ if (sf.getFeatureGroup() != null)
{
- tooltiptext.append(sequence.getDescription());
- tooltiptext.append("\n");
+ tooltiptext.append(sf.getFeatureGroup());
+ nl = true;
}
-
- SequenceFeature sf[] = sequence.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
+ if (sf.getType() != null)
{
- 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");
- }
- }
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getType());
+ nl = true;
+ }
+ if (sf.getDescription() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getDescription());
+ nl = true;
+ }
+ if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
+ {
+ tooltiptext.append(" Score = ");
+ tooltiptext.append(sf.getScore());
+ nl = true;
+ }
+ if (sf.getStatus() != null && sf.getStatus().length() > 0)
+ {
+ tooltiptext.append(" (");
+ tooltiptext.append(sf.getStatus());
+ tooltiptext.append(")");
+ nl = true;
+ }
+ if (nl)
+ {
+ tooltiptext.append("\n");
}
}
+
if (tooltiptext.length() == 0)
{
// nothing to display - so clear tooltip if one is visible
@@ -171,17 +169,19 @@ public class IdPanel extends Panel implements MouseListener,
}
if (tooltip == null)
{
- tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
- + tooltiptext.toString(), idCanvas);
+ tooltip = new Tooltip(
+ sequence.getDisplayId(true) + "\n" + tooltiptext.toString(),
+ idCanvas);
}
else
{
- tooltip.setTip(sequence.getDisplayId(true) + "\n"
- + tooltiptext.toString());
+ tooltip.setTip(
+ sequence.getDisplayId(true) + "\n" + tooltiptext.toString());
}
tooltiptext = null;
}
+ @Override
public void mouseDragged(MouseEvent e)
{
mouseDragging = true;
@@ -198,9 +198,10 @@ public class IdPanel extends Panel implements MouseListener,
}
lastid = seq;
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
}
+ @Override
public void mouseClicked(MouseEvent e)
{
if (e.getClickCount() < 2)
@@ -208,7 +209,7 @@ public class IdPanel extends Panel implements MouseListener,
return;
}
- // DEFAULT LINK IS FIRST IN THE LINK LIST
+ // get the sequence details
int seq = alignPanel.seqPanel.findSeq(e);
SequenceI sq = av.getAlignment().getSequenceAt(seq);
if (sq == null)
@@ -217,46 +218,15 @@ public class IdPanel extends Panel implements MouseListener,
}
String id = sq.getName();
- String target = null;
- String url = null;
- int i = 0;
- while (url == null && i < links.size())
+ // get the default url with the sequence details filled in
+ if (urlProvider == null)
{
- // 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();
- jalview.util.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];
+ return;
}
+ String url = urlProvider.getPrimaryUrl(id);
+ String target = urlProvider.getPrimaryTarget(id);
try
{
-
alignPanel.alignFrame.showURL(url, target);
} catch (Exception ex)
{
@@ -264,6 +234,7 @@ public class IdPanel extends Panel implements MouseListener,
}
}
+ @Override
public void mouseEntered(MouseEvent e)
{
if (scrollThread != null)
@@ -272,6 +243,7 @@ public class IdPanel extends Panel implements MouseListener,
}
}
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
@@ -279,18 +251,19 @@ public class IdPanel extends Panel implements MouseListener,
return;
}
- if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
+ if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
{
scrollThread = new ScrollThread(true);
}
if (mouseDragging && e.getY() >= getSize().height
- && av.getAlignment().getHeight() > av.getEndSeq())
+ && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
{
scrollThread = new ScrollThread(false);
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
if (e.getClickCount() > 1)
@@ -301,33 +274,37 @@ public class IdPanel extends Panel implements MouseListener,
int y = e.getY();
if (av.getWrapAlignment())
{
- y -= 2 * av.charHeight;
+ y -= 2 * av.getCharHeight();
}
int seq = alignPanel.seqPanel.findSeq(e);
- if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((e.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sq = 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++)
+ /*
+ * build a new links menu based on the current links
+ * and any non-positional features
+ */
+ List nlinks;
+ if (urlProvider != null)
{
- nlinks.addElement(links.elementAt(l));
+ nlinks = urlProvider.getLinksForMenu();
}
- SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
+ else
{
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ nlinks = new ArrayList<>();
+ }
+
+ for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
+ {
+ if (sf.links != null)
{
- if (sf[sl].links != null && sf[sl].links.size() > 0)
+ for (String link : sf.links)
{
- for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
- {
- nlinks.addElement(sf[sl].links.elementAt(l));
- }
+ nlinks.add(link);
}
}
}
@@ -339,8 +316,8 @@ public class IdPanel extends Panel implements MouseListener,
}
if ((av.getSelectionGroup() == null)
- || ((!e.isControlDown() && !e.isShiftDown()) && av
- .getSelectionGroup() != null))
+ || ((!jalview.util.Platform.isControlDown(e)
+ && !e.isShiftDown()) && av.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
@@ -356,7 +333,7 @@ public class IdPanel extends Panel implements MouseListener,
selectSeq(seq);
}
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
}
void selectSeq(int seq)
@@ -389,12 +366,13 @@ public class IdPanel extends Panel implements MouseListener,
}
for (int i = start; i <= end; i++)
{
- av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), i == end);
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ i == end);
}
}
+ @Override
public void mouseReleased(MouseEvent e)
{
if (scrollThread != null)
@@ -417,7 +395,7 @@ public class IdPanel extends Panel implements MouseListener,
{
idCanvas.setHighlighted(list);
- if (list == null)
+ if (list == null || list.isEmpty())
{
return;
}
@@ -425,9 +403,10 @@ public class IdPanel extends Panel implements MouseListener,
int index = av.getAlignment().findIndex(list.get(0));
// do we need to scroll the panel?
- if (av.getStartSeq() > index || av.getEndSeq() < index)
+ if (av.getRanges().getStartSeq() > index
+ || av.getRanges().getEndSeq() < index)
{
- alignPanel.setScrollValues(av.getStartRes(), index);
+ av.getRanges().setStartSeq(index);
}
}
@@ -438,9 +417,9 @@ public class IdPanel extends Panel implements MouseListener,
boolean up = true;
- public ScrollThread(boolean up)
+ public ScrollThread(boolean isUp)
{
- this.up = up;
+ this.up = isUp;
start();
}
@@ -449,18 +428,19 @@ public class IdPanel extends Panel implements MouseListener,
running = false;
}
+ @Override
public void run()
{
running = true;
while (running)
{
- if (alignPanel.scrollUp(up))
+ if (av.getRanges().scrollUp(up))
{
// scroll was ok, so add new sequence to selection
- int seq = av.getStartSeq();
+ int seq = av.getRanges().getStartSeq();
if (!up)
{
- seq = av.getEndSeq();
+ seq = av.getRanges().getEndSeq();
}
if (seq < lastid)
@@ -479,7 +459,7 @@ public class IdPanel extends Panel implements MouseListener,
running = false;
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
try
{
Thread.sleep(100);
@@ -489,5 +469,4 @@ public class IdPanel extends Panel implements MouseListener,
}
}
}
-
}