X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=4cc4a3a5d5e1fa4961532d1a75fb8cb4e47aee4f;hb=5078a67d8357697791d2e71f9df95a46e762aa2e;hp=eba52d562a8f820bd2d21acdeff62994ba6aab1a;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index eba52d5..4cc4a3a 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 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. * @@ -24,7 +24,9 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.util.UrlLink; +import jalview.urls.api.UrlProviderFactoryI; +import jalview.urls.api.UrlProviderI; +import jalview.urls.applet.AppletUrlProviderFactory; import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; @@ -33,8 +35,9 @@ 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; public class IdPanel extends Panel implements MouseListener, MouseMotionListener @@ -52,7 +55,7 @@ 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 +69,9 @@ 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 +79,27 @@ public class IdPanel extends Panel implements MouseListener, label = av.applet.getParameter("linkLabel_" + i); url = av.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 = av.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); @@ -188,6 +188,7 @@ public class IdPanel extends Panel implements MouseListener, tooltiptext = null; } + @Override public void mouseDragged(MouseEvent e) { mouseDragging = true; @@ -207,6 +208,7 @@ public class IdPanel extends Panel implements MouseListener, alignPanel.paintAlignment(false); } + @Override public void mouseClicked(MouseEvent e) { if (e.getClickCount() < 2) @@ -214,7 +216,7 @@ 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 +225,15 @@ 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) { @@ -270,6 +241,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mouseEntered(MouseEvent e) { if (scrollThread != null) @@ -278,6 +250,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -285,18 +258,19 @@ 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) @@ -318,10 +292,14 @@ 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++) + List nlinks; + if (urlProvider != null) + { + nlinks = urlProvider.getLinksForMenu(); + } + else { - nlinks.addElement(links.elementAt(l)); + nlinks = new ArrayList(); } SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures(); for (int sl = 0; sf != null && sl < sf.length; sl++) @@ -332,7 +310,7 @@ public class IdPanel extends Panel implements MouseListener, { for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++) { - nlinks.addElement(sf[sl].links.elementAt(l)); + nlinks.add(sf[sl].links.elementAt(l)); } } } @@ -345,8 +323,8 @@ 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 +379,7 @@ public class IdPanel extends Panel implements MouseListener, } + @Override public void mouseReleased(MouseEvent e) { if (scrollThread != null) @@ -431,9 +410,10 @@ 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); + alignPanel.setScrollValues(av.getRanges().getStartRes(), index); } } @@ -455,6 +435,7 @@ public class IdPanel extends Panel implements MouseListener, running = false; } + @Override public void run() { running = true; @@ -463,10 +444,10 @@ public class IdPanel extends Panel implements MouseListener, if (alignPanel.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)