X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=f8ea522eb225e3465b406875c6c3c322ab85d6ee;hb=d3cabbfdd38d554bb8a8b17d3e2c4b113c102545;hp=7981634355f84715fae6cd55cf38188c3ffb3108;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index 7981634..f8ea522 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 2.8.2) - * 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. * @@ -20,35 +20,41 @@ */ package jalview.appletgui; -import java.awt.*; -import java.awt.event.*; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.util.UrlProvider; +import jalview.util.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.*; -import jalview.util.UrlLink; - 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) { @@ -62,6 +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++) @@ -69,33 +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); @@ -138,7 +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()); @@ -184,6 +181,7 @@ public class IdPanel extends Panel implements MouseListener, tooltiptext = null; } + @Override public void mouseDragged(MouseEvent e) { mouseDragging = true; @@ -203,6 +201,7 @@ public class IdPanel extends Panel implements MouseListener, alignPanel.paintAlignment(false); } + @Override public void mouseClicked(MouseEvent e) { if (e.getClickCount() < 2) @@ -218,47 +217,55 @@ public class IdPanel extends Panel implements MouseListener, return; } String id = sq.getName(); + String url = urlProvider.getDefaultUrl(id); + String target = urlProvider.getDefaultTarget(id); - 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 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; + } - 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]; - } + if (urlLink.usesDBAccession()) + { + // this URL requires an accession id, not the name of a sequence + 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) { @@ -266,6 +273,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mouseEntered(MouseEvent e) { if (scrollThread != null) @@ -274,6 +282,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -293,6 +302,7 @@ public class IdPanel extends Panel implements MouseListener, } } + @Override public void mousePressed(MouseEvent e) { if (e.getClickCount() > 1) @@ -303,7 +313,7 @@ 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); @@ -314,11 +324,8 @@ 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.getLinksForDisplay(); + SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures(); for (int sl = 0; sf != null && sl < sf.length; sl++) { @@ -341,8 +348,8 @@ 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); @@ -397,6 +404,7 @@ public class IdPanel extends Panel implements MouseListener, } + @Override public void mouseReleased(MouseEvent e) { if (scrollThread != null) @@ -451,6 +459,7 @@ public class IdPanel extends Panel implements MouseListener, running = false; } + @Override public void run() { running = true; @@ -491,5 +500,4 @@ public class IdPanel extends Panel implements MouseListener, } } } - }