X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=feca8461cbd492a19e725a0e88eaee311fe506d1;hb=a889a61789f15e79ecde7043cddfdea18ad00166;hp=258b8b6b3891f7126f100afd388519b44e9a5aa1;hpb=bb8129c04f80504354b02b0876538ba680e11529;p=jalview.git diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index 258b8b6..feca846 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -20,22 +20,24 @@ */ package jalview.appletgui; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.urls.UrlProvider; +import jalview.urls.UrlProviderI; +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.HashMap; import java.util.List; import java.util.Vector; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.util.UrlLink; -import jalview.viewmodel.AlignmentViewport; - public class IdPanel extends Panel implements MouseListener, MouseMotionListener { @@ -52,7 +54,7 @@ public class IdPanel extends Panel implements MouseListener, boolean mouseDragging = false; - java.util.Vector links = new java.util.Vector(); + UrlProviderI urlProvider = null; public IdPanel(AlignViewport av, AlignmentPanel parent) { @@ -66,6 +68,9 @@ public class IdPanel extends Panel implements MouseListener, String label, url; // TODO: add in group link parameter + + // make a list of label,url pairs + HashMap urlList = new HashMap(); if (av.applet != null) { for (int i = 1; i < 10; i++) @@ -73,33 +78,21 @@ public class IdPanel extends Panel implements MouseListener, label = av.applet.getParameter("linkLabel_" + i); url = av.applet.getParameter("linkURL_" + i); - if (label != null && url != 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 = av.applet.getParameter("linkLabel_1"); + urlProvider = new UrlProvider(defaultUrl, urlList); } } - 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); @@ -142,7 +135,7 @@ public class IdPanel extends Panel implements MouseListener, nl = true; } ; - if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f) + if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f) { tooltiptext.append(" Score = "); tooltiptext.append(sf[sl].getScore()); @@ -188,6 +181,7 @@ public class IdPanel extends Panel implements MouseListener, tooltiptext = null; } + @Override public void mouseDragged(MouseEvent e) { mouseDragging = true; @@ -207,6 +201,7 @@ public class IdPanel extends Panel implements MouseListener, alignPanel.paintAlignment(false); } + @Override public void mouseClicked(MouseEvent e) { if (e.getClickCount() < 2) @@ -214,7 +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) @@ -223,46 +218,11 @@ 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()) - { - // 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]; - } + // get the default url with the sequence details filled in + String url = urlProvider.getDefaultUrl(id); + String target = urlProvider.getDefaultTarget(id); try { - alignPanel.alignFrame.showURL(url, target); } catch (Exception ex) { @@ -270,6 +230,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mouseEntered(MouseEvent e) { if (scrollThread != null) @@ -278,6 +239,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -297,6 +259,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mousePressed(MouseEvent e) { if (e.getClickCount() > 1) @@ -318,11 +281,8 @@ public class IdPanel extends Panel implements MouseListener, // 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)); - } + Vector nlinks = urlProvider.getLinksForMenu(); + SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures(); for (int sl = 0; sf != null && sl < sf.length; sl++) { @@ -345,8 +305,8 @@ 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); @@ -401,6 +361,7 @@ public class IdPanel extends Panel implements MouseListener, } + @Override public void mouseReleased(MouseEvent e) { if (scrollThread != null) @@ -455,6 +416,7 @@ public class IdPanel extends Panel implements MouseListener, running = false; } + @Override public void run() { running = true;