<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="src"/>
+ <classpathentry kind="src" path="utils"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="lib" path="lib/activation.jar"/>
<classpathentry kind="lib" path="lib/axis.jar" sourcepath="D:/axis-1_2RC2-src/axis-1_2RC2"/>
</classpathentry>
<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
- <classpathentry kind="lib" path="lib/min-jaba-client.jar"/>
<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
+ <classpathentry kind="lib" path="lib/min-jaba-client-2.0.jar" sourcepath="/clustengine2"/>
<classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
<classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
+ <classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
+ <classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
+ <classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
- <classpathentry exported="true" kind="con" path="GROOVY_DSL_SUPPORT"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.java"/>
+ <classpathentry kind="lib" path="/Users/jimp/git/jalview_clean/lib/VARNAv3-9-dev.jar"/>
<classpathentry kind="output" path="classes"/>
</classpath>
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*/
package jalview.bin;
+ import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+ import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+
import java.awt.Color;
import java.io.*;
import java.text.DateFormat;
import java.util.*;
import org.apache.log4j.*;
- import org.biojava.dasobert.dasregistry.Das1Source;
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* histogram.</li>
* <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
* logo.</li>
+ * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
+ * logo normalised to row height rather than histogram height.</li>
* <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
* </li>
System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
}
+ // LOAD THE AUTHORS FROM THE authors.props file
+ try
+ {
+ String authorDetails = "jar:".concat(Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString()
+ .concat("!/authors.props"));
+
+ java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading author details: " + ex);
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
+ }
+
// FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
// MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
// VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
}
/**
- * generate Das1Sources from the local das source list
- *
- * @return Vector of Das1Sources
- */
- public static Vector getLocalDasSources()
- {
- Vector localSources = new Vector();
- String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
- if (local != null)
- {
- StringTokenizer st = new StringTokenizer(local, "\t");
- while (st.hasMoreTokens())
- {
- String token = st.nextToken();
- int bar = token.indexOf("|");
- Das1Source source = new Das1Source();
- source.setUrl(token.substring(bar + 1));
- if (source.getUrl().startsWith("sequence:"))
- {
- source.setUrl(source.getUrl().substring(9));
- // this source also serves sequences as well as features
- source.setCapabilities(new String[]
- { "sequence", "features" });
- }
- else
- {
- // default is that all user added sources serve features
- source.setCapabilities(new String[]
- { "features" });
- }
-
- source.setNickname(token.substring(0, bar));
-
- localSources.addElement(source);
- }
- }
- return localSources;
- }
-
- /**
* GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
* enabled.
*/
}
return null;
}
+
+ private static DasSourceRegistryI sourceRegistry=null;
+ /**
+ * initialise and ..
+ * @return instance of the das source registry
+ */
+ public static DasSourceRegistryI getDasSourceRegistry()
+ {
+ if (sourceRegistry==null)
+ {
+ sourceRegistry = new DasSourceRegistry();
+ }
+ return sourceRegistry;
+ }
}
/*\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
* \r
*/\r
package jalview.gui;\r
\r
- import java.util.*;\r
- \r
- import java.awt.*;\r
- import java.awt.event.*;\r
- import javax.swing.*;\r
- import javax.swing.event.*;\r
- import javax.swing.table.*;\r
- \r
- import org.biojava.dasobert.dasregistry.*;\r
- import jalview.jbgui.*;\r
- import jalview.util.*;\r
+ import jalview.jbgui.GDasSourceBrowser;\r
+ import jalview.util.TableSorter;\r
+ import jalview.ws.dbsources.das.api.DasSourceRegistryI;\r
+ import jalview.ws.dbsources.das.api.jalviewSourceI;\r
+ \r
+ import java.awt.BorderLayout;\r
+ import java.awt.event.ActionEvent;\r
+ import java.awt.event.MouseAdapter;\r
+ import java.awt.event.MouseEvent;\r
+ import java.util.ArrayList;\r
+ import java.util.List;\r
+ import java.util.Properties;\r
+ import java.util.StringTokenizer;\r
+ import java.util.Vector;\r
+ \r
+ import javax.swing.JCheckBox;\r
+ import javax.swing.JLabel;\r
+ import javax.swing.JOptionPane;\r
+ import javax.swing.JPanel;\r
+ import javax.swing.JTextField;\r
+ import javax.swing.ListSelectionModel;\r
+ import javax.swing.SwingUtilities;\r
+ import javax.swing.event.ListSelectionEvent;\r
+ import javax.swing.event.ListSelectionListener;\r
+ import javax.swing.table.AbstractTableModel;\r
+ \r
+ import org.biodas.jdas.schema.sources.CAPABILITY;\r
+ import org.biodas.jdas.schema.sources.COORDINATES;\r
+ import org.biodas.jdas.schema.sources.PROP;\r
+ import org.biodas.jdas.schema.sources.VERSION;\r
\r
public class DasSourceBrowser extends GDasSourceBrowser implements\r
Runnable, ListSelectionListener\r
{\r
- static DasSource[] dasSources = null;\r
- \r
- Hashtable localSources = null;\r
- \r
- Vector selectedSources;\r
- \r
- public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";\r
- \r
- /**\r
- * true if thread is running and we are talking to DAS registry service\r
- */\r
- public boolean loadingDasSources = false;\r
+ DasSourceRegistryI sourceRegistry = null;\r
\r
- protected static String getDasRegistryURL()\r
- {\r
- String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
- DEFAULT_REGISTRY);\r
- \r
- if (registry.indexOf("/registry/das1/sources/") > -1)\r
- {\r
- jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,\r
- DEFAULT_REGISTRY);\r
- registry = DEFAULT_REGISTRY;\r
- }\r
- return registry;\r
- }\r
+ Vector<String> selectedSources;\r
\r
public DasSourceBrowser(FeatureSettings featureSettings)\r
{\r
fs = featureSettings;\r
- String registry = getDasRegistryURL();\r
+ // TODO DasSourceRegistryProvider API\r
+ sourceRegistry = jalview.bin.Cache.getDasSourceRegistry();\r
+ String registry = sourceRegistry.getDasRegistryURL();\r
\r
registryURL.setText(registry);\r
\r
}\r
});\r
\r
- if (dasSources != null)\r
+ if (sourceRegistry.getSources() != null)\r
{\r
init();\r
}\r
\r
FeatureSettings fs = null;\r
\r
+ private boolean loadingDasSources;\r
+ \r
public DasSourceBrowser()\r
{\r
this(null);\r
\r
public void paintComponent(java.awt.Graphics g)\r
{\r
- if (dasSources == null && !loadingDasSources)\r
+ if (sourceRegistry == null)\r
{\r
Thread worker = new Thread(this);\r
worker.start();\r
\r
void init()\r
{\r
- int dSize = dasSources.length;\r
+ List<jalviewSourceI> sources = sourceRegistry.getSources();\r
+ int dSize = sources.size();\r
Object[][] data = new Object[dSize][2];\r
for (int i = 0; i < dSize; i++)\r
{\r
- data[i][0] = dasSources[i].getNickname();\r
- data[i][1] = new Boolean(selectedSources.contains(dasSources[i]\r
- .getNickname()));\r
+ data[i][0] = sources.get(i).getTitle(); // what's equivalent of nickname\r
+ data[i][1] = new Boolean(selectedSources.contains(sources.get(i).getTitle()));\r
}\r
\r
refreshTableData(data);\r
- setCapabilities(dasSources);\r
+ setCapabilities(sourceRegistry);\r
\r
javax.swing.SwingUtilities.invokeLater(new Runnable()\r
{\r
return;\r
}\r
\r
- int dSize = dasSources.length;\r
- for (int i = 0; i < dSize; i++)\r
+ int dSize = sourceRegistry.getSources().size();\r
+ for (jalviewSourceI ds : sourceRegistry.getSources())\r
{\r
- if (!dasSources[i].getNickname().equals(nickName))\r
+ if (!ds.getTitle().equals(nickName))\r
{\r
continue;\r
}\r
\r
- DasSource ds = dasSources[i];\r
- \r
- text.append("<font color=\"#0000FF\">Id:</font> "\r
- + dasSources[i].getId() + "<br>");\r
+ VERSION latest = ds.getVersion();\r
+ text.append("<font color=\"#0000FF\">Id:</font> " + ds.getUri()\r
+ + "<br>");\r
text.append("<font color=\"#0000FF\">Nickname:</font> "\r
- + dasSources[i].getNickname() + "<br>");\r
- text.append("<font color=\"#0000FF\">URL:</font> "\r
- + dasSources[i].getUrl() + "<br>");\r
- \r
+ + ds.getTitle() + "<br>");\r
+ \r
+ if (!ds.isLocal())\r
+ {\r
+ // TODO: IMMEDIATE verify that URI + ds.URI point to latest version for non-local sources.\r
+ if (ds.getDocHref()!=null) {\r
+ text.append("<font color=\"#0000FF\">URL:</font> " + ds.getDocHref()\r
+ + "<br>");\r
+ }\r
+ \r
text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"\r
- + dasSources[i].getAdminemail()\r
- + "\">"\r
- + dasSources[i].getAdminemail() + "</a>" + "<br>");\r
+ + ds.getEmail() + "\">" + ds.getEmail() + "</a>" + "<br>");\r
\r
text.append("<font color=\"#0000FF\">Registered at:</font> "\r
- + dasSources[i].getRegisterDate() + "<br>");\r
- \r
- text.append("<font color=\"#0000FF\">Last successful test:</font> "\r
- + dasSources[i].getLeaseDate() + "<br>");\r
+ + latest.getCreated() + "<br>");\r
\r
+ // TODO: Identify last successful test date\r
+ // text.append("<font color=\"#0000FF\">Last successful test:</font> "\r
+ // + latest.dasSources[i].getLeaseDate() + "<br>");\r
+ } else {\r
+ text.append("Source was added manually.<br/>");\r
+ }\r
text.append("<font color=\"#0000FF\">Labels:</font> ");\r
- for (int s = 0; s < dasSources[i].getLabels().length; s++)\r
+ boolean b = false;\r
+ for (PROP labl : latest.getPROP())\r
{\r
- text.append(dasSources[i].getLabels()[s]);\r
- if (s < dasSources[i].getLabels().length - 1)\r
+ if (labl.getName().equalsIgnoreCase("LABEL"))\r
{\r
- text.append(",");\r
+ if (!b)\r
+ {\r
+ text.append(",");\r
+ }\r
+ text.append(" ");\r
+ \r
+ text.append(labl.getValue());\r
+ b = true;\r
}\r
- text.append(" ");\r
+ ;\r
}\r
text.append("<br>");\r
\r
text.append("<font color=\"#0000FF\">Capabilities:</font> ");\r
- String[] scap = dasSources[i].getCapabilities();\r
+ CAPABILITY[] scap = latest.getCAPABILITY().toArray(new CAPABILITY[0]);\r
for (int j = 0; j < scap.length; j++)\r
{\r
- text.append(scap[j]);\r
+ text.append(scap[j].getType());\r
if (j < scap.length - 1)\r
{\r
text.append(", ");\r
text.append("<br>");\r
\r
text.append("<font color=\"#0000FF\">Coordinates:</font> ");\r
- DasCoordinateSystem[] dcs = ds.getCoordinateSystem();\r
- for (int j = 0; j < dcs.length; j++)\r
+ for (COORDINATES dcs : latest.getCOORDINATES())\r
{\r
- text.append("(" + dcs[j].getUniqueId() + ") "\r
- + dcs[j].getCategory() + ", " + dcs[j].getName());\r
- if (dcs[j].getNCBITaxId() != 0)\r
+ text.append("(" + dcs.getUri() + ") "\r
+ \r
+ + dcs.getSource() + ", " + dcs.getAuthority());\r
+ if (dcs.getTaxid() != null && dcs.getTaxid().trim().length() > 0)\r
{\r
- text.append(", " + dcs[j].getNCBITaxId());\r
+ text.append(", " + dcs.getTaxid());\r
}\r
- if (dcs[j].getOrganismName().length() > 0)\r
+ if (dcs.getVersion()!=null && dcs.getVersion().trim().length() > 0)\r
{\r
- text.append(", " + dcs[j].getOrganismName());\r
- }\r
+ {\r
+ text.append(", " + dcs.getVersion());\r
+ }\r
\r
- text.append("<br>");\r
- }\r
+ text.append("<br>");\r
+ }\r
\r
- text.append("<font color=\"#0000FF\">Description:</font> "\r
- + dasSources[i].getDescription() + "<br>");\r
+ text.append("<font color=\"#0000FF\">Description:</font> "\r
+ + ds.getDescription() + "<br>");\r
\r
- if (dasSources[i].getHelperurl() != null\r
- && dasSources[i].getHelperurl().length() > 0)\r
- {\r
- text.append("<font color=\"#0000FF\"><a href=\""\r
- + dasSources[i].getHelperurl()\r
- + "\">Go to site</a></font<br>");\r
- }\r
+ if (ds.getDocHref() != null && ds.getDocHref().length() > 0)\r
+ {\r
+ text.append("<font color=\"#0000FF\"><a href=\""\r
+ + ds.getDocHref() + "\">Go to site</a></font<br>");\r
+ }\r
\r
- text.append("</font></html>");\r
+ text.append("</font></html>");\r
\r
- break;\r
+ break;\r
+ }\r
}\r
- \r
fullDetails.setText(text.toString());\r
javax.swing.SwingUtilities.invokeLater(new Runnable()\r
{\r
progressBar.setIndeterminate(true);\r
setParentGuiEnabled(false);\r
// Refresh the source list.\r
- dasSources = null;\r
- getDASSource();\r
+ sourceRegistry.refreshSources();\r
\r
init();\r
\r
}\r
}\r
\r
- public Vector getSelectedSources()\r
+ public Vector<jalviewSourceI> getSelectedSources()\r
{\r
// wait around if we're still loading.\r
- while (dasSources == null)\r
+ while (sourceRegistry == null)\r
{\r
if (!loadingDasSources)\r
{\r
}\r
}\r
\r
- Vector selected = new Vector();\r
- for (int r = 0; r < selectedSources.size(); r++)\r
+ Vector<jalviewSourceI> selected = new Vector<jalviewSourceI>();\r
+ for (String source : selectedSources)\r
{\r
- for (int i = 0; i < dasSources.length; i++)\r
+ jalviewSourceI srce = sourceRegistry.getSource(source);\r
+ if (srce != null)\r
{\r
- if (dasSources[i].getNickname()\r
- .equals(selectedSources.elementAt(r)))\r
- {\r
- selected.addElement(dasSources[i]);\r
- break;\r
- }\r
+ selected.addElement(srce);\r
}\r
}\r
return selected;\r
}\r
\r
- /**\r
- * retrieve das sources from registry and add local source list\r
- * \r
- * @return\r
- */\r
- public DasSource[] getDASSource()\r
- {\r
- if (dasSources == null)\r
- {\r
- dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();\r
- appendLocalSources();\r
- }\r
- \r
- return dasSources;\r
- }\r
- \r
public void refresh_actionPerformed(ActionEvent e)\r
{\r
saveProperties(jalview.bin.Cache.applicationProperties);\r
worker.start();\r
}\r
\r
- private void setCapabilities(DasSource[] sources)\r
+ private void setCapabilities(DasSourceRegistryI sourceRegistry2)\r
{\r
- Vector authority = new Vector();\r
- Vector type = new Vector();\r
- Vector label = new Vector();\r
- \r
- authority.addElement("Any");\r
- type.addElement("Any");\r
- label.addElement("Any");\r
+ Vector<String> authority = new Vector<String>();\r
+ Vector<String> type = new Vector<String>();\r
+ Vector<String> label = new Vector<String>();\r
+ Vector<String> taxIds = new Vector<String>();\r
+ authority.add("Any");\r
+ type.add("Any");\r
+ label.add("Any");\r
\r
- for (int i = 0; i < sources.length; i++)\r
+ for (jalviewSourceI ds : sourceRegistry2.getSources())\r
{\r
- DasSource ds = sources[i];\r
+ VERSION latest = ds.getVersion();\r
\r
- DasCoordinateSystem[] dcs = ds.getCoordinateSystem();\r
- \r
- for (int j = 0; j < dcs.length; j++)\r
+ for (COORDINATES cs : latest.getCOORDINATES())\r
{\r
- if (!type.contains(dcs[j].getCategory()))\r
+ if (!type.contains(cs.getSource()))\r
{\r
- type.addElement(dcs[j].getCategory());\r
+ type.add(cs.getSource()); // source==category\r
}\r
\r
- if (!authority.contains(dcs[j].getName()))\r
+ if (!authority.contains(cs.getAuthority()))\r
{\r
- authority.addElement(dcs[j].getName());\r
+ authority.add(cs.getAuthority());\r
}\r
}\r
\r
- String[] slabels = ds.getLabels();\r
- for (int s = 0; s < slabels.length; s++)\r
+ for (PROP slabel : latest.getPROP())\r
{\r
- if (!label.contains(slabels[s]))\r
+ if (slabel.getName().equalsIgnoreCase("LABEL")\r
+ && !label.contains(slabel.getValue()))\r
{\r
- label.addElement(slabels[s]);\r
+ label.add(slabel.getValue());\r
}\r
}\r
\r
filter1.setListData(authority);\r
filter2.setListData(type);\r
filter3.setListData(label);\r
+ // filter4 taxIds\r
\r
javax.swing.SwingUtilities.invokeLater(new Runnable()\r
{\r
{\r
int selectedRow = table.getSelectionModel().getMinSelectionIndex();\r
nickname = table.getValueAt(selectedRow, 0).toString();\r
- url = ((DasSource) localSources.get(nickname)).getUrl();\r
- seqsrc = ((DasSource) localSources.get(nickname))\r
- .hasCapability("sequence");\r
+ jalviewSourceI source = sourceRegistry.getSource(nickname);\r
+ url = source.getUri();\r
+ seqsrc = source.isSequenceSource();\r
}\r
\r
JTextField nametf = new JTextField(nickname, 40);\r
urltf.setText(urltf.getText() + "/");\r
}\r
\r
- Das1Source local = new Das1Source();\r
+ jalviewSourceI local = sourceRegistry.createLocalSource(\r
+ urltf.getText(), nametf.getText(), seqs.isSelected(), true);\r
+ List sources = sourceRegistry.getSources();\r
+ int osize = sources.size();\r
+ int size = osize + (newSource ? 1 : 0);\r
\r
- local.setUrl(urltf.getText());\r
- local.setNickname(nametf.getText());\r
- if (seqs.isSelected())\r
+ Object[][] data = new Object[size][2];\r
+ DASTableModel dtm = (table != null) ? (DASTableModel)((TableSorter) table.getModel()).getTableModel()\r
+ : null;\r
+ for (int i = 0; i < osize; i++)\r
{\r
- local.setCapabilities(new String[]\r
- { "features", "sequence" });\r
- }\r
- if (localSources == null)\r
- {\r
- localSources = new Hashtable();\r
- }\r
- \r
- localSources.put(local.getNickname(), local);\r
- \r
- if (!newSource && !nickname.equals(nametf.getText()))\r
- {\r
- localSources.remove(nickname);\r
- }\r
- \r
- int size = dasSources.length;\r
- int adjust = newSource ? 1 : 0;\r
- \r
- Object[][] data = new Object[size + adjust][2];\r
- for (int i = 0; i < size; i++)\r
- {\r
- if (!newSource && dasSources[i].getNickname().equals(nickname))\r
+ String osrc = (dtm == null || i >= osize) ? null : (String) dtm\r
+ .getValueAt(i, 0);\r
+ if (!newSource && osrc != null\r
+ && dtm.getValueAt(i, 0).equals(nickname))\r
{\r
- ((DasSource) dasSources[i]).setNickname(local.getNickname());\r
- ((DasSource) dasSources[i]).setUrl(local.getUrl());\r
- data[i][0] = local.getNickname();\r
+ data[i][0] = local.getTitle();\r
data[i][1] = new Boolean(true);\r
}\r
else\r
{\r
- data[i][0] = dasSources[i].getNickname();\r
- data[i][1] = new Boolean(selectedSources.contains(dasSources[i]\r
- .getNickname()));\r
+ data[i][0] = osrc;\r
+ data[i][1] = new Boolean(selectedSources.contains(osrc));\r
}\r
}\r
- \r
+ // Always add a new source at the end\r
if (newSource)\r
{\r
- data[size][0] = local.getNickname();\r
- data[size][1] = new Boolean(true);\r
- selectedSources.add(local.getNickname());\r
+ data[osize][0] = local.getTitle();\r
+ data[osize][1] = new Boolean(true);\r
+ selectedSources.add(local.getTitle());\r
}\r
\r
- DasSource[] tmp = new DasSource[size + adjust];\r
- \r
- System.arraycopy(dasSources, 0, tmp, 0, size);\r
- \r
- if (newSource)\r
- {\r
- tmp[size] = local;\r
- }\r
- \r
- dasSources = tmp;\r
- \r
refreshTableData(data);\r
\r
SwingUtilities.invokeLater(new Runnable()\r
}\r
});\r
\r
- displayFullDetails(local.getNickname());\r
+ displayFullDetails(local.getTitle());\r
}\r
\r
public void editRemoveLocalSource(MouseEvent evt)\r
\r
String nickname = table.getValueAt(selectedRow, 0).toString();\r
\r
- if (!localSources.containsKey(nickname))\r
+ if (!sourceRegistry.getSource(nickname).isLocal())\r
{\r
JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
"You can only edit or remove local DAS Sources!",\r
amendLocal(false);\r
break;\r
case 1:\r
- localSources.remove(nickname);\r
+ sourceRegistry.removeLocalSource(sourceRegistry.getSource(nickname));\r
selectedSources.remove(nickname);\r
- Object[][] data = new Object[dasSources.length - 1][2];\r
- DasSource[] tmp = new DasSource[dasSources.length - 1];\r
- int index = 0;\r
- for (int i = 0; i < dasSources.length; i++)\r
+ Object[][] data = new Object[sourceRegistry.getSources().size()][2];\r
+ int index = 0,\r
+ l = table.getRowCount();\r
+ \r
+ for (int i = 0; i < l; i++)\r
{\r
- if (dasSources[i].getNickname().equals(nickname))\r
+ String nm;\r
+ if ((nm = (String) table.getValueAt(i, 0)).equals(nickname))\r
{\r
continue;\r
}\r
else\r
{\r
- tmp[index] = dasSources[i];\r
- data[index][0] = dasSources[i].getNickname();\r
- data[index][1] = new Boolean(\r
- selectedSources.contains(dasSources[i].getNickname()));\r
+ data[index][0] = nm;\r
+ data[index][1] = new Boolean(selectedSources.contains(nm));\r
index++;\r
}\r
}\r
- dasSources = tmp;\r
refreshTableData(data);\r
SwingUtilities.invokeLater(new Runnable()\r
{\r
}\r
}\r
\r
- void appendLocalSources()\r
- {\r
- if (localSources == null)\r
- {\r
- return;\r
- }\r
- // note - we add all das sources to list so they can be filtered for the\r
- // standard fetchDbRefs function\r
- int size = dasSources != null ? dasSources.length : 0;\r
- int lsize = localSources.size();\r
- \r
- Object[][] data = new Object[size + lsize][2];\r
- for (int i = 0; i < size; i++)\r
- {\r
- data[i][0] = dasSources[i].getNickname();\r
- data[i][1] = new Boolean(selectedSources.contains(dasSources[i]\r
- .getNickname()));\r
- }\r
- \r
- DasSource[] tmp = new DasSource[size + lsize];\r
- if (dasSources != null)\r
- {\r
- System.arraycopy(dasSources, 0, tmp, 0, size);\r
- }\r
- \r
- Enumeration en = localSources.keys();\r
- int index = size;\r
- while (en.hasMoreElements())\r
- {\r
- String key = en.nextElement().toString();\r
- data[index][0] = key;\r
- data[index][1] = new Boolean(false);\r
- tmp[index] = new Das1Source();\r
- tmp[index].setNickname(key);\r
- tmp[index].setUrl(((DasSource) localSources.get(key)).getUrl());\r
- \r
- index++;\r
- }\r
- \r
- dasSources = tmp;\r
- \r
- refreshTableData(data);\r
- }\r
- \r
public void valueChanged(ListSelectionEvent evt)\r
{\r
// Called when the MainTable selection changes\r
displayFullDetails(null);\r
\r
// Filter the displayed data sources\r
\r
ArrayList names = new ArrayList();\r
ArrayList selected = new ArrayList();\r
- DasSource ds;\r
\r
// The features filter is not visible, but we must still\r
// filter the das source list here.\r
// July 2006 - only 6 sources fo not serve features\r
Object[] dummyFeatureList = new Object[]\r
{ "features" };\r
- \r
- for (int i = 0; i < dSize; i++)\r
+ List<jalviewSourceI> srcs=sourceRegistry.getSources();\r
+ for (jalviewSourceI ds : srcs)\r
{\r
- ds = dasSources[i];\r
- DasCoordinateSystem[] dcs = ds.getCoordinateSystem();\r
\r
- if (dcs.length == 0 && ds.getCapabilities().length == 0\r
+ VERSION v = ds.getVersion();\r
+ List<COORDINATES> coords = v.getCOORDINATES();\r
+ if (ds.isLocal() || ((coords == null || coords.size() == 0)\r
&& filter1.getSelectedIndex() == 0\r
&& filter2.getSelectedIndex() == 0\r
- && filter3.getSelectedIndex() == 0)\r
+ && filter3.getSelectedIndex() == 0))\r
{\r
// THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT\r
// HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT\r
// IS ADDED FROM THE REGISTRY\r
- names.add(ds.getNickname());\r
- selected.add(new Boolean(selectedSources.contains(ds.getNickname())));\r
+ names.add(ds.getTitle());\r
+ selected.add(new Boolean(selectedSources.contains(ds.getTitle())));\r
continue;\r
}\r
\r
- if (!selectedInList(dummyFeatureList, ds.getCapabilities())\r
+ if (!selectedInList(dummyFeatureList, ds.getCapabilityList(v))\r
|| !selectedInList(filter3.getSelectedValues(),\r
- ds.getLabels()))\r
+ ds.getLabelsFor(v)))\r
{\r
continue;\r
}\r
\r
- for (int j = 0; j < dcs.length; j++)\r
+ for (int j = 0; j < coords.size(); j++)\r
{\r
if (selectedInList(filter1.getSelectedValues(), new String[]\r
- { dcs[j].getName() })\r
+ { coords.get(j).getAuthority() })\r
&& selectedInList(filter2.getSelectedValues(), new String[]\r
- { dcs[j].getCategory() }))\r
+ { coords.get(j).getSource() }))\r
{\r
- names.add(ds.getNickname());\r
- selected.add(new Boolean(selectedSources.contains(ds\r
- .getNickname())));\r
+ names.add(ds.getTitle());\r
+ selected.add(new Boolean(selectedSources.contains(ds.getTitle())));\r
break;\r
}\r
}\r
}\r
\r
- dSize = names.size();\r
+ int dSize = names.size();\r
Object[][] data = new Object[dSize][2];\r
for (int d = 0; d < dSize; d++)\r
{\r
refreshTableData(data);\r
}\r
\r
- boolean selectedInList(Object[] selection, String[] items)\r
+ private boolean selectedInList(Object[] selection, String[] items)\r
{\r
for (int i = 0; i < selection.length; i++)\r
{\r
{\r
return true;\r
}\r
- \r
+ if (items==null || items.length==0)\r
+ {\r
+ return false;\r
+ }\r
+ String sel=(items[0].startsWith("das1:") ? "das1:":"")+selection[i];\r
for (int j = 0; j < items.length; j++)\r
{\r
- if (selection[i].equals(items[j]))\r
+ if (sel.equals(items[j]))\r
{\r
return true;\r
}\r
{\r
selectedSources.addElement(st.nextToken());\r
}\r
- \r
- Vector _localSources = jalview.bin.Cache.getLocalDasSources();\r
- if (_localSources != null)\r
- {\r
- if (localSources == null)\r
- {\r
- localSources = new Hashtable();\r
- }\r
- Enumeration sources = _localSources.elements();\r
- while (sources.hasMoreElements())\r
- {\r
- Das1Source source = (Das1Source) sources.nextElement();\r
- localSources.put(source.getNickname(), source);\r
- }\r
- }\r
}\r
\r
public void reset_actionPerformed(ActionEvent e)\r
{\r
- registryURL.setText(DEFAULT_REGISTRY);\r
+ registryURL.setText(sourceRegistry.getDasRegistryURL());\r
}\r
\r
/**\r
properties.setProperty(jalview.bin.Cache.DAS_ACTIVE_SOURCE,\r
sb.toString());\r
\r
- if (localSources != null)\r
- {\r
- sb = new StringBuffer();\r
- Enumeration en = localSources.keys();\r
- while (en.hasMoreElements())\r
- {\r
- String token = en.nextElement().toString();\r
- sb.append(token\r
- + "|"\r
- + (((DasSource) localSources.get(token))\r
- .hasCapability("sequence") ? "sequence:" : "")\r
- + ((DasSource) localSources.get(token)).getUrl() + "\t");\r
- }\r
- \r
- properties.setProperty(jalview.bin.Cache.DAS_LOCAL_SOURCE,\r
- sb.toString());\r
- }\r
- \r
+ String sourceprop = sourceRegistry.getLocalSourceString();\r
+ properties.setProperty(jalview.bin.Cache.DAS_LOCAL_SOURCE, sourceprop);\r
}\r
\r
class DASTableModel extends AbstractTableModel\r
}\r
});\r
thr.start();\r
- while (loadingDasSources || dasSources == null)\r
+ while (loadingDasSources || sourceRegistry == null)\r
{\r
try\r
{\r
}\r
}\r
\r
- public Vector resolveSourceNicknames(Vector sources)\r
- {\r
- \r
- Vector resolved = new Vector();\r
- if (sources != null)\r
- {\r
- for (int i = 0; i < dasSources.length; i++)\r
- {\r
- if (sources.contains(dasSources[i].getNickname()))\r
- {\r
- if (!resolved.contains(dasSources[i]))\r
- {\r
- resolved.addElement(dasSources[i]);\r
- }\r
- }\r
- }\r
- }\r
- return resolved;\r
- }\r
- \r
/**\r
* disable or enable the buttons on the source browser\r
* \r
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.io.*;
import java.util.*;
+ import java.util.List;
import java.awt.*;
import java.awt.event.*;
- import java.awt.geom.AffineTransform;
- import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import jalview.io.*;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
+ import jalview.ws.dbsources.das.api.jalviewSourceI;
public class FeatureSettings extends JPanel
{
Vector allGroups = new Vector();
SequenceFeature[] tmpfeatures;
String group;
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
+ if (af.getViewport().getAlignment().getSequenceAt(i).getDatasetSequence()
.getSequenceFeatures() == null)
{
continue;
}
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
int index = 0;
// Find out which features should be visible depending on which groups
// are selected / deselected
// and recompute average width ordering
- for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+ for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
.getDatasetSequence().getSequenceFeatures();
if (tmpfeatures == null)
{
* @param checkDbRefs
* @param promptFetchDbRefs
*/
- private void doDasFeatureFetch(Vector selectedSources,
+ private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
boolean checkDbRefs, boolean promptFetchDbRefs)
{
SequenceI[] dataset, seqs;
* Vector of Strings to resolve to DAS source nicknames.
* @return sources that are present in source list.
*/
- public Vector resolveSourceNicknames(Vector sources)
+ public List<jalviewSourceI> resolveSourceNicknames(Vector sources)
{
- return dassourceBrowser.resolveSourceNicknames(sources);
+ return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
}
/**
public void fetchDasFeatures(Vector sources, boolean block)
{
initDasSources();
- Vector resolved = resolveSourceNicknames(sources);
+ List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
if (resolved.size() == 0)
{
resolved = dassourceBrowser.getSelectedSources();
}
if (resolved.size() > 0)
{
- final Vector dassources = resolved;
+ final List<jalviewSourceI> dassources = resolved;
fetchDAS.setEnabled(false);
// cancelDAS.setEnabled(true); doDasFetch does this.
Runnable fetcher = new Runnable()
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*/
package jalview.gui;
- import java.io.*;
import java.util.*;
import java.awt.*;
import javax.swing.*;
- import MCview.*;
import jalview.datamodel.*;
- import jalview.datamodel.xdb.embl.*;
- import java.io.File;
import jalview.io.*;
- import jalview.ws.DBRefFetcher;
- import jalview.ws.ebi.EBIFetchClient;
- import jalview.ws.seqfetcher.ASequenceFetcher;
+ import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.seqfetcher.DbSourceProxy;
- import java.awt.Rectangle;
import java.awt.BorderLayout;
- import java.awt.Dimension;
public class SequenceFetcher extends JPanel implements Runnable
{
private static jalview.ws.SequenceFetcher sfetch = null;
- private static String dasRegistry = null;
+ private static DasSourceRegistryI dasRegistry = null;
private static boolean _initingFetcher = false;
}
}
if (sfetch == null
- || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+ || dasRegistry != jalview.bin.Cache.getDasSourceRegistry())
{
_initingFetcher = true;
initingThread = Thread.currentThread();
guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
Thread.currentThread().hashCode());
}
- dasRegistry = DasSourceBrowser.getDasRegistryURL();
+ dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+ dasRegistry.refreshSources();
+
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
if (guiWindow != null)
{
{
for (int i = 0; i < al.getHeight(); i++)
{
- alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this
+ alignFrame.viewport.getAlignment().addSequence(al.getSequenceAt(i)); // this
// also
// creates
// dataset
// sequence
// entries
}
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
.getHeight());
- alignFrame.viewport.alignment.getWidth();
+ alignFrame.viewport.getAlignment().getWidth();
alignFrame.viewport.firePropertyChange("alignment", null,
alignFrame.viewport.getAlignment().getSequences());
}
/*\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
* \r
import jalview.gui.Desktop;\r
import jalview.gui.IProgressIndicator;\r
import jalview.gui.OOMWarning;\r
+ import jalview.ws.dbsources.das.api.jalviewSourceI;\r
\r
import java.lang.reflect.Array;\r
import java.util.Enumeration;\r
import java.util.StringTokenizer;\r
import java.util.Vector;\r
\r
- import org.biojava.dasobert.dasregistry.DasSource;\r
- \r
import uk.ac.ebi.picr.model.UPEntry;\r
\r
/**\r
{\r
// af.featureSettings_actionPerformed(null);\r
String[] defdb = null, otherdb = sfetcher\r
- .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
+ .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);\r
Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings\r
.getSelectedSources() : new jalview.gui.DasSourceBrowser()\r
.getSelectedSources();\r
Enumeration en = dasselsrc.elements();\r
while (en.hasMoreElements())\r
{\r
- DasSource src = (DasSource) en.nextElement();\r
- selsources.addElement(src.getNickname());\r
+ jalviewSourceI src = (jalviewSourceI) en.nextElement();\r
+ selsources.addElement(src.getTitle());\r
}\r
int osel = 0;\r
for (int o = 0; otherdb != null && o < otherdb.length; o++)\r
}\r
// append additional sources\r
String[] otherdb = sfetcher\r
- .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
+ .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);\r
if (otherdb != null && otherdb.length > 0)\r
{\r
String[] newsrc = new String[dbSources.length + otherdb.length];\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
* \r
*/\r
package jalview.ws;\r
\r
- import java.net.*;\r
- import java.util.*;\r
- \r
- import javax.swing.*;\r
- \r
- import org.biojava.dasobert.das.*;\r
- import org.biojava.dasobert.das2.*;\r
- import org.biojava.dasobert.das2.io.*;\r
- import org.biojava.dasobert.dasregistry.*;\r
- import org.biojava.dasobert.eventmodel.*;\r
import jalview.bin.Cache;\r
- import jalview.datamodel.*;\r
- import jalview.gui.*;\r
+ import jalview.datamodel.DBRefEntry;\r
+ import jalview.datamodel.SequenceFeature;\r
+ import jalview.datamodel.SequenceI;\r
+ import jalview.gui.AlignFrame;\r
+ import jalview.gui.Desktop;\r
+ import jalview.gui.FeatureSettings;\r
import jalview.util.UrlLink;\r
+ import jalview.ws.dbsources.das.api.DasSourceRegistryI;\r
+ import jalview.ws.dbsources.das.api.jalviewSourceI;\r
+ \r
+ import java.util.ArrayList;\r
+ import java.util.Enumeration;\r
+ import java.util.HashMap;\r
+ import java.util.HashSet;\r
+ import java.util.Iterator;\r
+ import java.util.List;\r
+ import java.util.Map;\r
+ import java.util.Set;\r
+ import java.util.StringTokenizer;\r
+ import java.util.Vector;\r
+ \r
+ import javax.swing.JOptionPane;\r
+ \r
+ import org.biodas.jdas.client.adapters.features.DasGFFAdapter;\r
+ import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter;\r
+ import org.biodas.jdas.client.threads.FeaturesClientMultipleSources;\r
+ import org.biodas.jdas.schema.features.ERRORSEGMENT;\r
+ import org.biodas.jdas.schema.features.FEATURE;\r
+ import org.biodas.jdas.schema.features.LINK;\r
+ import org.biodas.jdas.schema.features.SEGMENT;\r
+ import org.biodas.jdas.schema.features.TYPE;\r
+ import org.biodas.jdas.schema.features.UNKNOWNFEATURE;\r
+ import org.biodas.jdas.schema.features.UNKNOWNSEGMENT;\r
+ import org.biodas.jdas.schema.sources.COORDINATES;\r
\r
/**\r
* DOCUMENT ME!\r
\r
StringBuffer sbuffer = new StringBuffer();\r
\r
- Vector selectedSources;\r
+ List<jalviewSourceI> selectedSources;\r
\r
boolean cancelled = false;\r
\r
\r
long startTime;\r
\r
+ private DasSourceRegistryI sourceRegistry;\r
+ \r
/**\r
* Creates a new SequenceFeatureFetcher object. Uses default\r
* \r
}\r
\r
public DasSequenceFeatureFetcher(SequenceI[] oursequences,\r
- FeatureSettings fsettings, Vector ourselectedSources,\r
+ FeatureSettings fsettings, List<jalviewSourceI> selectedSources2,\r
boolean checkDbrefs, boolean promptFetchDbrefs)\r
{\r
- this.selectedSources = new Vector();\r
- Enumeration sources = ourselectedSources.elements();\r
+ this.selectedSources = new ArrayList<jalviewSourceI>();\r
// filter both sequences and sources to eliminate duplicates\r
- while (sources.hasMoreElements())\r
+ for (jalviewSourceI src : selectedSources2)\r
{\r
- Object src = sources.nextElement();\r
if (!selectedSources.contains(src))\r
{\r
- selectedSources.addElement(src);\r
+ selectedSources.add(src);\r
}\r
;\r
}\r
af.setShowSeqFeatures(true);\r
}\r
int uniprotCount = 0;\r
- for (int i = 0; i < selectedSources.size(); i++)\r
+ for (jalviewSourceI source : selectedSources)\r
{\r
- DasSource source = (DasSource) selectedSources.elementAt(i);\r
- DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
- for (int c = 0; c < coords.length; c++)\r
+ for (COORDINATES coords : source.getVersion().getCOORDINATES())\r
{\r
// TODO: match UniProt coord system canonically (?) - does\r
// UniProt==uniprot==UNIPROT ?\r
- if (coords[c].getName().indexOf("UniProt") > -1)\r
+ if (coords.getAuthority().toLowerCase().equals("uniprot"))\r
{\r
uniprotCount++;\r
break;\r
}\r
else\r
{\r
- startFetching();\r
+ _startFetching();\r
}\r
}\r
else\r
{\r
- startFetching();\r
+ _startFetching();\r
}\r
\r
}\r
- \r
+ private void _startFetching()\r
+ {\r
+ new Thread(new FetchSeqFeatures()).start();\r
+ }\r
+ class FetchSeqFeatures implements Runnable\r
+ {\r
+ public void run()\r
+ {\r
+ startFetching();\r
+ setGuiFetchComplete();\r
+ }\r
+ }\r
class FetchDBRefs implements Runnable\r
{\r
public void run()\r
{\r
new DBRefFetcher(sequences, af).fetchDBRefs(true);\r
startFetching();\r
+ setGuiFetchComplete();\r
}\r
}\r
\r
/**\r
- * Spawns a number of dasobert Fetcher threads to add features to sequences in\r
- * the dataset\r
+ * Spawns Fetcher threads to add features to sequences in the dataset\r
*/\r
void startFetching()\r
{\r
{\r
af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
}\r
- \r
+ if (sourceRegistry == null)\r
+ {\r
+ sourceRegistry = Cache.getDasSourceRegistry();\r
+ }\r
if (selectedSources == null || selectedSources.size() == 0)\r
{\r
try\r
{\r
- DasSource[] sources = new jalview.gui.DasSourceBrowser()\r
- .getDASSource();\r
- \r
+ jalviewSourceI[] sources = sourceRegistry.getSources().toArray(\r
+ new jalviewSourceI[0]);\r
String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",\r
"uniprot");\r
StringTokenizer st = new StringTokenizer(active, "\t");\r
token = st.nextToken();\r
for (int i = 0; i < sources.length; i++)\r
{\r
- if (sources[i].getNickname().equals(token))\r
+ if (sources[i].getTitle().equals(token))\r
{\r
- selectedSources.addElement(sources[i]);\r
+ selectedSources.add(sources[i]);\r
break;\r
}\r
}\r
}\r
\r
sourcesRemaining = selectedSources.size();\r
+ FeaturesClientMultipleSources fc = new FeaturesClientMultipleSources();\r
+ fc.setConnProps(sourceRegistry.getSessionHandler());\r
// Now sending requests one at a time to each server\r
- for (int sourceIndex = 0; sourceIndex < selectedSources.size()\r
- && !cancelled; sourceIndex++)\r
+ ArrayList<jalviewSourceI> srcobj = new ArrayList<jalviewSourceI>();\r
+ ArrayList<String> src = new ArrayList<String>();\r
+ List<List<String>> ids = new ArrayList<List<String>>();\r
+ List<List<DBRefEntry>> idobj = new ArrayList<List<DBRefEntry>>();\r
+ List<Map<String, SequenceI>> sqset = new ArrayList<Map<String, SequenceI>>();\r
+ for (jalviewSourceI _sr : selectedSources)\r
+ {\r
+ \r
+ Map<String, SequenceI> slist = new HashMap<String, SequenceI>();\r
+ List<DBRefEntry> idob = new ArrayList<DBRefEntry>();\r
+ List<String> qset = new ArrayList<String>();\r
+ \r
+ for (SequenceI seq : sequences)\r
+ {\r
+ Object[] idset = nextSequence(_sr, seq);\r
+ if (idset != null)\r
+ {\r
+ List<DBRefEntry> _idob = (List<DBRefEntry>) idset[0];\r
+ List<String> _qset = (List<String>) idset[1];\r
+ if (_idob.size() > 0)\r
+ {\r
+ // add sequence's ref for each id derived from it\r
+ // (space inefficient, but most unambiguous)\r
+ // could replace with hash with _qset values as keys.\r
+ Iterator<DBRefEntry> dbobj = _idob.iterator();\r
+ for (String q : _qset)\r
+ {\r
+ SequenceI osq = slist.get(q);\r
+ DBRefEntry dr = dbobj.next();\r
+ if (osq != null && osq != seq)\r
+ {\r
+ // skip - non-canonical query\r
+ }\r
+ else\r
+ {\r
+ idob.add(dr);\r
+ qset.add(q);\r
+ slist.put(q, seq);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (idob.size() > 0)\r
+ {\r
+ srcobj.add(_sr);\r
+ src.add(_sr.getSourceURL());\r
+ ids.add(qset);\r
+ idobj.add(idob);\r
+ sqset.add(slist);\r
+ }\r
+ }\r
+ Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();\r
+ Map<String, Map<List<String>, DasGFFAdapter>> results = new HashMap<String, Map<List<String>, DasGFFAdapter>>();\r
+ fc.fetchData(src, ids, false, results, errors);\r
+ fc.shutDown();\r
+ while (!fc.isTerminated())\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(200);\r
+ } catch (InterruptedException x)\r
+ {\r
+ \r
+ }\r
+ }\r
+ Iterator<List<String>> idset = ids.iterator();\r
+ Iterator<List<DBRefEntry>> idobjset = idobj.iterator();\r
+ Iterator<Map<String, SequenceI>> seqset = sqset.iterator();\r
+ for (jalviewSourceI source : srcobj)\r
+ {\r
+ processResponse(seqset.next(), source, idset.next(), idobjset.next(),\r
+ results.get(source.getSourceURL()),\r
+ errors.get(source.getSourceURL()));\r
+ }\r
+ }\r
+ \r
+ private void processResponse(Map<String, SequenceI> sequencemap,\r
+ jalviewSourceI jvsource, List<String> ids,\r
+ List<DBRefEntry> idobj, Map<List<String>, DasGFFAdapter> results,\r
+ Map<List<String>, Exception> errors)\r
+ {\r
+ Set<SequenceI> sequences = new HashSet<SequenceI>();\r
+ String source = jvsource.getSourceURL();\r
+ // process features\r
+ DasGFFAdapter result = (results == null) ? null : results.get(ids);\r
+ Exception error = (errors == null) ? null : errors.get(ids);\r
+ if (result == null)\r
+ {\r
+ debug("das source " + source + " could not be contacted. "\r
+ + (error == null ? "" : error.toString()));\r
+ }\r
+ else\r
{\r
- DasSource dasSource = (DasSource) selectedSources\r
- .elementAt(sourceIndex);\r
\r
- nextSequence(dasSource, sequences[0]);\r
+ GFFAdapter gff = result.getGFF();\r
+ List<SEGMENT> segments = gff.getSegments();\r
+ List<ERRORSEGMENT> errorsegs = gff.getErrorSegments();\r
+ List<UNKNOWNFEATURE> unkfeats = gff.getUnknownFeatures();\r
+ List<UNKNOWNSEGMENT> unksegs = gff.getUnknownSegments();\r
+ debug("das source " + source + " returned " + gff.getTotal()\r
+ + " responses. " + (errorsegs != null ? errorsegs.size() : 0)\r
+ + " were incorrect segment queries, "\r
+ + (unkfeats != null ? unkfeats.size() : 0)\r
+ + " were unknown features "\r
+ + (unksegs != null ? unksegs.size() : 0)\r
+ + " were unknown segments and "\r
+ + (segments != null ? segments.size() : 0)\r
+ + " were segment responses.");\r
+ Iterator<DBRefEntry> dbr = idobj.iterator();\r
+ if (segments != null)\r
+ {\r
+ for (SEGMENT seg : segments)\r
+ {\r
+ String id = seg.getId();\r
+ DBRefEntry dbref = idobj.get(ids.indexOf(id));\r
+ SequenceI sequence = sequencemap.get(id);\r
+ boolean added = false;\r
+ sequences.add(sequence);\r
+ \r
+ for (FEATURE feat : seg.getFEATURE())\r
+ {\r
+ // standard DAS feature-> jalview sequence feature transformation\r
+ SequenceFeature f = newSequenceFeature(feat, jvsource.getTitle());\r
+ if (!parseSeqFeature(sequence, f, feat, jvsource))\r
+ {\r
+ if (dbref.getMap() != null && f.getBegin() > 0\r
+ && f.getEnd() > 0)\r
+ {\r
+ debug("mapping from " + f.getBegin() + " - " + f.getEnd());\r
+ SequenceFeature vf[] = null;\r
+ \r
+ try\r
+ {\r
+ vf = dbref.getMap().locateFeature(f);\r
+ } catch (Exception ex)\r
+ {\r
+ Cache.log\r
+ .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");\r
+ Cache.log.info("Mapping feature from " + f.getBegin()\r
+ + " to " + f.getEnd() + " in dbref "\r
+ + dbref.getAccessionId() + " in "\r
+ + dbref.getSource());\r
+ Cache.log.info("using das Source " + source);\r
+ Cache.log.info("Exception", ex);\r
+ }\r
+ \r
+ if (vf != null)\r
+ {\r
+ for (int v = 0; v < vf.length; v++)\r
+ {\r
+ debug("mapping to " + v + ": " + vf[v].getBegin()\r
+ + " - " + vf[v].getEnd());\r
+ sequence.addSequenceFeature(vf[v]);\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ sequence.addSequenceFeature(f);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ featuresAdded(sequences);\r
+ }\r
+ else\r
+ {\r
+ // System.out.println("No features found for " + seq.getName()\r
+ // + " from: " + e.getDasSource().getNickname());\r
+ }\r
}\r
}\r
\r
\r
int sourcesRemaining = 0;\r
\r
- void responseComplete(DasSource dasSource, SequenceI seq)\r
- {\r
- if (seq != null)\r
- {\r
- for (int seqIndex = 0; seqIndex < sequences.length - 1 && !cancelled; seqIndex++)\r
- {\r
- if (sequences[seqIndex] == seq)\r
- {\r
- nextSequence(dasSource, sequences[++seqIndex]);\r
- return;\r
- }\r
- }\r
- }\r
- \r
- sourcesRemaining--;\r
- \r
- if (sourcesRemaining == 0)\r
- {\r
- System.err.println("Fetching Complete.");\r
- setGuiFetchComplete();\r
- }\r
- \r
- }\r
- \r
private void setGuiFetchComplete()\r
{\r
\r
}\r
}\r
\r
- void featuresAdded(SequenceI seq)\r
+ void featuresAdded(Set<SequenceI> seqs)\r
{\r
if (af == null)\r
{\r
int index;\r
for (index = start; index < end; index++)\r
{\r
- if (seq == af.getViewport().getAlignment().getSequenceAt(index)\r
- .getDatasetSequence())\r
+ for (SequenceI seq : seqs)\r
{\r
- af.alignPanel.paintAlignment(true);\r
- break;\r
+ if (seq == af.getViewport().getAlignment().getSequenceAt(index)\r
+ .getDatasetSequence())\r
+ {\r
+ af.alignPanel.paintAlignment(true);\r
+ index = end;\r
+ break;\r
+ }\r
}\r
}\r
}\r
\r
- void nextSequence(DasSource dasSource, SequenceI seq)\r
+ Object[] nextSequence(jalviewSourceI dasSource, SequenceI seq)\r
{\r
if (cancelled)\r
- return;\r
+ return null;\r
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(\r
seq.getDBRef(), new String[]\r
{\r
// TODO: minimal list of DAS queries to make by querying with untyped ID if\r
// distinct from any typed IDs\r
\r
+ List<DBRefEntry> ids = new ArrayList<DBRefEntry>();\r
+ List<String> qstring = new ArrayList<String>();\r
boolean dasCoordSysFound = false;\r
\r
if (uprefs != null)\r
// do any of these ids match the source's coordinate system ?\r
for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)\r
{\r
- DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
\r
- for (int csIndex = 0; csIndex < cs.length && !dasCoordSysFound; csIndex++)\r
+ for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())\r
{\r
- if (cs.length > 0\r
- && jalview.util.DBRefUtils.isDasCoordinateSystem(\r
- cs[csIndex].getName(), uprefs[j]))\r
+ if (jalview.util.DBRefUtils.isDasCoordinateSystem(\r
+ csys.getAuthority(), uprefs[j]))\r
{\r
debug("Launched fetcher for coordinate system "\r
- + cs[0].getName());\r
+ + csys.getAuthority());\r
// Will have to pass any mapping information to the fetcher\r
// - the start/end for the DBRefEntry may not be the same as the\r
// sequence's start/end\r
\r
System.out.println(seq.getName() + " "\r
+ (seq.getDatasetSequence() == null) + " "\r
- + dasSource.getUrl());\r
+ + csys.getUri());\r
\r
dasCoordSysFound = true; // break's out of the loop\r
- createFeatureFetcher(seq, dasSource, uprefs[j]);\r
+ ids.add(uprefs[j]);\r
+ qstring.add(uprefs[j].getAccessionId());\r
}\r
else\r
- System.out.println("IGNORE " + cs[csIndex].getName());\r
+ System.out.println("IGNORE " + csys.getAuthority());\r
}\r
}\r
}\r
}\r
if (id != null)\r
{\r
+ DBRefEntry dbre = new DBRefEntry();\r
+ dbre.setAccessionId(id);\r
// Should try to call a general feature fetcher that\r
// queries many sources with name to discover applicable ID references\r
- createFeatureFetcher(seq, dasSource, id);\r
- }\r
- }\r
- \r
- }\r
- \r
- /**\r
- * fetch and add das features to a sequence using the given source URL and\r
- * compatible DbRef id. new features are mapped using the DbRef mapping to the\r
- * local coordinate system.\r
- * \r
- * @param seq\r
- * @param SourceUrl\r
- * @param dbref\r
- */\r
- protected void createFeatureFetcher(final SequenceI seq,\r
- final DasSource dasSource, final DBRefEntry dbref)\r
- {\r
- \r
- // ////////////\r
- // / fetch DAS features\r
- final Das1Source source = new Das1Source();\r
- source.setUrl(dasSource.getUrl());\r
- source.setNickname(dasSource.getNickname());\r
- if (dbref == null || dbref.getAccessionId() == null\r
- || dbref.getAccessionId().length() < 1)\r
- {\r
- responseComplete(dasSource, seq); // reduce thread count anyhow\r
- return;\r
- }\r
- debug("new Das Feature Fetcher for " + dbref.getSource() + ":"\r
- + dbref.getAccessionId() + " querying " + dasSource.getUrl());\r
- FeatureThread fetcher = new FeatureThread(dbref.getAccessionId()\r
- // + ":" + start + "," + end,\r
- , source);\r
- \r
- fetcher.addFeatureListener(new FeatureListener()\r
- {\r
- public void comeBackLater(FeatureEvent e)\r
- {\r
- responseComplete(dasSource, seq);\r
- debug("das source " + e.getSource().getNickname()\r
- + " asked us to come back in " + e.getComeBackLater()\r
- + " secs.");\r
- }\r
- \r
- public void newFeatures(FeatureEvent e)\r
- {\r
- \r
- Das1Source ds = e.getSource();\r
- \r
- Map[] features = e.getFeatures();\r
- // add features to sequence\r
- debug("das source " + ds.getUrl() + " returned " + features.length\r
- + " features");\r
- \r
- if (features.length > 0)\r
- {\r
- for (int i = 0; i < features.length; i++)\r
- {\r
- // standard DAS feature-> jalview sequence feature transformation\r
- SequenceFeature f = newSequenceFeature(features[i],\r
- source.getNickname());\r
- if (!parseSeqFeature(seq, f, features[i], source))\r
- {\r
- if (dbref.getMap() != null && f.getBegin() > 0\r
- && f.getEnd() > 0)\r
- {\r
- debug("mapping from " + f.getBegin() + " - " + f.getEnd());\r
- SequenceFeature vf[] = null;\r
- \r
- try\r
- {\r
- vf = dbref.getMap().locateFeature(f);\r
- } catch (Exception ex)\r
- {\r
- Cache.log\r
- .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");\r
- Cache.log.info("Mapping feature from " + f.getBegin()\r
- + " to " + f.getEnd() + " in dbref "\r
- + dbref.getAccessionId() + " in "\r
- + dbref.getSource());\r
- Cache.log.info("using das Source " + ds.getUrl());\r
- Cache.log.info("Exception", ex);\r
- }\r
- \r
- if (vf != null)\r
- {\r
- for (int v = 0; v < vf.length; v++)\r
- {\r
- debug("mapping to " + v + ": " + vf[v].getBegin()\r
- + " - " + vf[v].getEnd());\r
- seq.addSequenceFeature(vf[v]);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- seq.addSequenceFeature(f);\r
- }\r
- }\r
- }\r
- featuresAdded(seq);\r
- }\r
- else\r
- {\r
- // System.out.println("No features found for " + seq.getName()\r
- // + " from: " + e.getDasSource().getNickname());\r
- }\r
- responseComplete(dasSource, seq);\r
- \r
+ ids.add(dbre);\r
+ qstring.add(dbre.getAccessionId());\r
}\r
}\r
\r
- );\r
- \r
- fetcher.start();\r
- }\r
- \r
- protected void createFeatureFetcher(final SequenceI seq,\r
- final DasSource dasSource, String id)\r
- {\r
- // ////////////\r
- // / fetch DAS features\r
- final Das1Source source = new Das1Source();\r
- source.setUrl(dasSource.getUrl());\r
- source.setNickname(dasSource.getNickname());\r
- \r
- if (id != null)\r
- {\r
- id = id.trim();\r
- }\r
- if (id != null && id.length() > 0)\r
- {\r
- debug("new Das Feature Fetcher for " + id + " querying "\r
- + dasSource.getUrl());\r
- FeatureThread fetcher = new FeatureThread(id\r
- // + ":" + start + "," + end,\r
- , source);\r
- \r
- fetcher.addFeatureListener(new FeatureListener()\r
- {\r
- public void comeBackLater(FeatureEvent e)\r
- {\r
- responseComplete(dasSource, seq);\r
- debug("das source " + e.getSource().getNickname()\r
- + " asked us to come back in " + e.getComeBackLater()\r
- + " secs.");\r
- }\r
- \r
- public void newFeatures(FeatureEvent e)\r
- {\r
- \r
- Das1Source ds = e.getSource();\r
- \r
- Map[] features = e.getFeatures();\r
- // add features to sequence\r
- debug("das source " + ds.getUrl() + " returned "\r
- + features.length + " features");\r
- \r
- if (features.length > 0)\r
- {\r
- for (int i = 0; i < features.length; i++)\r
- {\r
- // standard DAS feature-> jalview sequence feature transformation\r
- SequenceFeature f = newSequenceFeature(features[i],\r
- source.getNickname());\r
- if (!parseSeqFeature(seq, f, features[i], source))\r
- {\r
- // just add as a simple sequence feature\r
- seq.addSequenceFeature(f);\r
- }\r
- }\r
- \r
- featuresAdded(seq);\r
- }\r
- else\r
- {\r
- // System.out.println("No features found for " + seq.getName()\r
- // + " from: " + e.getDasSource().getNickname());\r
- }\r
- responseComplete(dasSource, seq);\r
- \r
- }\r
- }\r
- \r
- );\r
- \r
- fetcher.start();\r
- }\r
- else\r
- {\r
- // invalid fetch - indicate it is finished.\r
- debug("Skipping empty ID for querying " + dasSource.getUrl());\r
- responseComplete(dasSource, seq);\r
- }\r
+ return new Object[]\r
+ { ids, qstring };\r
}\r
\r
/**\r
* @return true if feature was consumed as another kind of annotation.\r
*/\r
protected boolean parseSeqFeature(SequenceI seq, SequenceFeature f,\r
- Map map, Das1Source source)\r
+ FEATURE feature, jalviewSourceI source)\r
{\r
SequenceI mseq = seq;\r
while (seq.getDatasetSequence() != null)\r
// try to parse the accession out\r
\r
DBRefEntry dbr = new DBRefEntry();\r
- dbr.setVersion(source.getNickname());\r
+ dbr.setVersion(source.getTitle());\r
StringTokenizer st = new StringTokenizer(f.getDescription(), ":");\r
if (st.hasMoreTokens())\r
{\r
/**\r
* creates a jalview sequence feature from a das feature document\r
* \r
- * @param dasfeature\r
+ * @param feat\r
* @return sequence feature object created using dasfeature information\r
*/\r
- SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
+ SequenceFeature newSequenceFeature(FEATURE feat, String nickname)\r
{\r
- if (dasfeature == null)\r
+ if (feat == null)\r
{\r
return null;\r
}\r
* qName.equals("SCORE")\r
*/\r
String desc = new String();\r
- if (dasfeature.containsKey("NOTE"))\r
+ if (feat.getNOTE() != null)\r
{\r
- desc += (String) dasfeature.get("NOTE");\r
+ for (String note : feat.getNOTE())\r
+ {\r
+ desc += (String) note;\r
+ }\r
}\r
\r
int start = 0, end = 0;\r
\r
try\r
{\r
- start = Integer.parseInt(dasfeature.get("START").toString());\r
+ start = Integer.parseInt(feat.getSTART().toString());\r
} catch (Exception ex)\r
{\r
}\r
try\r
{\r
- end = Integer.parseInt(dasfeature.get("END").toString());\r
+ end = Integer.parseInt(feat.getEND().toString());\r
} catch (Exception ex)\r
{\r
}\r
try\r
{\r
- Object scr = dasfeature.get("SCORE");\r
+ Object scr = feat.getSCORE();\r
if (scr != null)\r
{\r
score = (float) Double.parseDouble(scr.toString());\r
}\r
\r
SequenceFeature f = new SequenceFeature(\r
- (String) dasfeature.get("TYPE"), desc, start, end, score,\r
+ getTypeString(feat.getTYPE()), desc, start, end, score,\r
nickname);\r
\r
- if (dasfeature.containsKey("LINK"))\r
+ if (feat.getLINK() != null)\r
{\r
- // Do not put feature extent in link text for non-positional features\r
- if (f.begin == 0 && f.end == 0)\r
- {\r
- f.addLink(f.getType() + "|" + dasfeature.get("LINK"));\r
- }\r
- else\r
+ for (LINK link : feat.getLINK())\r
{\r
- f.addLink(f.getType() + " " + f.begin + "_" + f.end + "|"\r
- + dasfeature.get("LINK"));\r
+ // Do not put feature extent in link text for non-positional features\r
+ if (f.begin == 0 && f.end == 0)\r
+ {\r
+ f.addLink(f.getType() + " " + link.getContent() + "|"\r
+ + link.getHref());\r
+ }\r
+ else\r
+ {\r
+ f.addLink(f.getType() + " " + f.begin + "_" + f.end + " "\r
+ + link.getContent() + "|" + link.getHref());\r
+ }\r
}\r
}\r
\r
System.out.println("ERRR " + e);\r
e.printStackTrace();\r
System.out.println("############");\r
- debug("Failed to parse " + dasfeature.toString(), e);\r
+ debug("Failed to parse " + feat.toString(), e);\r
return null;\r
}\r
}\r
\r
- /**\r
- * query the default DAS Source Registry for sources. Uses value of jalview\r
- * property DAS_REGISTRY_URL and the DasSourceBrowser.DEFAULT_REGISTRY if that\r
- * doesn't exist.\r
- * \r
- * @return list of sources\r
- */\r
- public static DasSource[] getDASSources()\r
- {\r
- \r
- String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
- DasSourceBrowser.DEFAULT_REGISTRY);\r
- return getDASSources(registryURL);\r
- }\r
- \r
- /**\r
- * query the given URL for DasSources.\r
- * \r
- * @param registryURL\r
- * return sources from registryURL\r
- */\r
- public static DasSource[] getDASSources(String registryURL)\r
+ private String getTypeString(TYPE type)\r
{\r
- DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
- \r
- try\r
- {\r
- URL url = new URL(registryURL);\r
- \r
- DasSource[] sources = reader.readDasSource(url);\r
- \r
- List das1sources = new ArrayList();\r
- for (int i = 0; i < sources.length; i++)\r
- {\r
- DasSource ds = sources[i];\r
- if (ds instanceof Das2Source)\r
- {\r
- Das2Source d2s = (Das2Source) ds;\r
- if (d2s.hasDas1Capabilities())\r
- {\r
- Das1Source d1s = DasSourceConverter.toDas1Source(d2s);\r
- das1sources.add(d1s);\r
- }\r
- \r
- }\r
- else if (ds instanceof Das1Source)\r
- {\r
- das1sources.add((Das1Source) ds);\r
- }\r
- }\r
- \r
- return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources\r
- .size()]);\r
- } catch (Exception ex)\r
- {\r
- System.err.println("Failed to contact DAS1 registry at "\r
- + registryURL);\r
- ex.printStackTrace();\r
- return null;\r
- }\r
+ return type.getContent();\r
}\r
\r
}\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
* \r
*/\r
package jalview.ws;\r
\r
- import java.util.ArrayList;\r
- import java.util.Enumeration;\r
- import java.util.Vector;\r
- \r
- import org.biojava.dasobert.das2.Das2Source;\r
- import org.biojava.dasobert.dasregistry.Das1Source;\r
- import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
- import org.biojava.dasobert.dasregistry.DasSource;\r
- \r
import jalview.datamodel.Alignment;\r
import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.DBRefSource;\r
import jalview.datamodel.SequenceI;\r
- import jalview.ws.dbsources.DasSequenceSource;\r
+ import jalview.ws.dbsources.das.api.jalviewSourceI;\r
import jalview.ws.seqfetcher.ASequenceFetcher;\r
import jalview.ws.seqfetcher.DbSourceProxy;\r
\r
+ import java.util.ArrayList;\r
+ import java.util.Enumeration;\r
+ import java.util.List;\r
+ import java.util.Vector;\r
+ \r
/**\r
* This is the the concrete implementation of the sequence retrieval interface\r
* and abstract class in jalview.ws.seqfetcher. This implements the run-time\r
// alignment is\r
// 'default' for\r
// PFAM\r
+ addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);\r
+ addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);\r
registerDasSequenceSources();\r
}\r
\r
for (int i = 0; i < srcs.length; i++)\r
{\r
String nm = getSourceProxy(srcs[i]).getDbName();\r
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.DasSequenceSource)\r
+ if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)\r
{\r
if (nm.startsWith("das:"))\r
{\r
*/\r
public void registerDasSequenceSources()\r
{\r
- DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher\r
- .getDASSources();\r
- if (sources != null)\r
- {\r
- for (int s = 0; sources != null && s < sources.length; s++)\r
- {\r
- addDasSequenceSource(sources[s]);\r
- }\r
- }\r
- \r
- Vector localsources = jalview.bin.Cache.getLocalDasSources();\r
- if (localsources != null)\r
- {\r
- for (Enumeration ls = localsources.elements(); ls.hasMoreElements();)\r
- {\r
- addDasSequenceSource((DasSource) ls.nextElement());\r
- }\r
- }\r
- }\r
- \r
- /**\r
- * Try to create and add a DasSequenceSource to the list of sources.\r
- * \r
- * @param source\r
- * @return null if no source was added, or the new DasSequenceSource created\r
- */\r
- DasSequenceSource addDasSequenceSource(DasSource source)\r
- {\r
- DasSequenceSource ds = null;\r
- Das1Source d1s = null;\r
- if (source.hasCapability("sequence"))\r
- {\r
- if (source instanceof Das2Source)\r
- {\r
- if (((Das2Source) source).hasDas1Capabilities())\r
- {\r
- try\r
- {\r
- d1s = org.biojava.dasobert.das2.DasSourceConverter\r
- .toDas1Source((Das2Source) source);\r
- } catch (Exception e)\r
- {\r
- System.err.println("Ignoring DAS2 sequence source "\r
- + source.getNickname()\r
- + " - couldn't map to Das1Source.\n");\r
- e.printStackTrace();\r
- }\r
- }\r
- }\r
- else\r
- {\r
- if (source instanceof Das1Source)\r
- {\r
- d1s = (Das1Source) source;\r
- }\r
- }\r
- }\r
- if (d1s != null)\r
+ // TODO: define a context as a registry provider (either desktop,\r
+ // jalview.bin.cache, or something else).\r
+ for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry().getSources())\r
{\r
- DasCoordinateSystem[] css = d1s.getCoordinateSystem();\r
- if (css == null || css.length == 0)\r
+ if (source.isSequenceSource())\r
{\r
- // TODO: query das source directly to identify coordinate system... or\r
- // have to make up a coordinate system\r
- css = new DasCoordinateSystem[]\r
- { new DasCoordinateSystem() };\r
- css[0].setName(d1s.getNickname());\r
- css[0].setUniqueId(d1s.getNickname());\r
- }\r
- for (int c = 0; c < css.length; c++)\r
- {\r
- try\r
+ List<DbSourceProxy> dassources = source.getSequenceSourceProxies();\r
+ for (DbSourceProxy seqsrc : dassources)\r
{\r
- addDbRefSourceImpl(ds = new DasSequenceSource("das:"\r
- + d1s.getNickname() + " (" + css[c].getName() + ")",\r
- css[c].getName(), d1s, css[c]));\r
- } catch (Exception e)\r
- {\r
- System.err.println("Ignoring sequence coord system " + c + " ("\r
- + css[c].getName() + ") for source " + d1s.getNickname()\r
- + "- threw exception when constructing fetcher.\n");\r
- e.printStackTrace();\r
+ addDbRefSourceImpl(seqsrc);\r
}\r
}\r
}\r
- return ds;\r
}\r
}\r
/*\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
* \r
* database (unify with io)\r
* \r
* @author JimP\r
- * \r
+ * TODO: promote to API\r
*/\r
public interface DbSourceProxy\r
{\r
git://source.jalview.org / jalview.git / commitdiff