X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3c694646faeb8e2a3d2353b0024c345c11053956;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=dfcd807cd2e2ddb31af2ed05c8a1c4b69caeaa8f;hpb=0e2054d29bc49351f000d478659dc3c4371b251c;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index dfcd807..3c69464 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,25 +1,33 @@
/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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.bin;
-import java.awt.FlowLayout;
-import java.awt.Frame;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.HtmlSvgOutput;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
+
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.BufferedReader;
@@ -29,6 +37,7 @@ import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.lang.reflect.Constructor;
+import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
import java.net.URLDecoder;
@@ -37,12 +46,12 @@ import java.security.CodeSource;
import java.security.PermissionCollection;
import java.security.Permissions;
import java.security.Policy;
-import java.util.*;
-
-import javax.swing.*;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Vector;
-import jalview.gui.*;
-import jalview.util.Platform;
+import javax.swing.UIManager;
+import javax.swing.UnsupportedLookAndFeelException;
/**
* Main class for Jalview Application
@@ -71,11 +80,6 @@ public class Jalview
}
});
}
- /**
- * Put protein=true for get a protein example
- */
- private static boolean protein=false;
-
/**
* main class for Jalview application
@@ -90,61 +94,46 @@ public class Jalview
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
- if (new Platform().isAMac())
- {
- System.setProperty("com.apple.mrj.application.apple.menu.about.name",
- "Jalview");
- System.setProperty("apple.laf.useScreenMenuBar", "true");
- }
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
if (aparser.contains("help") || aparser.contains("h"))
{
- System.out
- .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
- + "-nodisplay\tRun Jalview without User Interface.\n"
- + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
- + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
- + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
- + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
- + "-features FILE\tUse the given file to mark features on the alignment.\n"
- + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
- + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
- + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
- + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
- + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
- + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
- + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
- + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
- + "-png FILE\tCreate PNG image FILE from alignment.\n"
- + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
- + "-eps FILE\tCreate EPS file FILE from alignment.\n"
- + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
- + "-noquestionnaire\tTurn off questionnaire check.\n"
- + "-nousagestats\tTurn off google analytics tracking for this session.\n"
- + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
- // +
- // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
- + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
- + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
- + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
- + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
- // +
- // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
- // + "-vses vamsas-session\tJoin session with given URN\n"
- + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
- + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ showUsage();
System.exit(0);
}
- if (aparser.contains("nodisplay") || aparser.contains("nogui") || aparser.contains("headless"))
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
{
System.setProperty("java.awt.headless", "true");
- headless=true;
+ headless = true;
}
- Cache.loadProperties(aparser.getValue("props")); // must do this before
+ String usrPropsFile = aparser.getValue("props");
+ Cache.loadProperties(usrPropsFile); // must do this before
+ if (usrPropsFile != null)
+ {
+ System.out.println("CMD [-props " + usrPropsFile
+ + "] executed successfully!");
+ }
+
// anything else!
+
+ final String jabawsUrl = aparser.getValue("jabaws");
+ if (jabawsUrl != null)
+ {
+ try
+ {
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ System.out.println("CMD [-jabaws " + jabawsUrl
+ + "] executed successfully!");
+ } catch (MalformedURLException e)
+ {
+ System.err.println("Invalid jabaws parameter: " + jabawsUrl
+ + " ignored");
+ }
+ }
+
String defs = aparser.getValue("setprop");
while (defs != null)
{
@@ -167,7 +156,8 @@ public class Jalview
{
headless = true;
}
- System.setProperty("http.agent", "Jalview Desktop/"+Cache.getDefault("VERSION", "Unknown"));
+ System.setProperty("http.agent",
+ "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
try
{
Cache.initLogger();
@@ -188,6 +178,21 @@ public class Jalview
} catch (Exception ex)
{
}
+ if (new Platform().isAMac())
+ {
+ System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+ "Jalview");
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ try
+ {
+ UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
+ .getLookAndFeel());
+ } catch (UnsupportedLookAndFeelException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
if (!headless)
{
@@ -199,6 +204,11 @@ public class Jalview
{
startUsageStats(desktop);
}
+ else
+ {
+ System.err.println("CMD [-nousagestats] executed successfully!");
+ }
+
if (!aparser.contains("noquestionnaire"))
{
String url = aparser.getValue("questionnaire");
@@ -208,6 +218,8 @@ public class Jalview
// questionnaire
Cache.log.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
+ System.out.println("CMD questionnaire[-" + url
+ + "] executed successfully!");
}
else
{
@@ -226,11 +238,20 @@ public class Jalview
}
}
}
+ else
+ {
+ System.err.println("CMD [-noquestionnaire] executed successfully!");
+ }
desktop.checkForNews();
}
+ if (!isHeadlessMode())
+ {
+ BioJsHTMLOutput.updateBioJS();
+ }
+
String file = null, protocol = null, format = null, data = null;
- jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+ jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
Vector getFeatures = null; // vector of das source nicknames to fetch
// features from
// loading is done.
@@ -336,10 +357,11 @@ public class Jalview
{
if (!headless)
{
- desktop.setProgressBar("Processing commandline arguments...",
+ desktop.setProgressBar(MessageManager
+ .getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
- System.out.println("Opening file: " + file);
+ System.out.println("CMD [-open " + file + "] executed successfully!");
if (!file.startsWith("http://"))
{
@@ -365,7 +387,7 @@ public class Jalview
}
else
{
-
+ Desktop.setCurrentAlignFrame(af);
data = aparser.getValue("colour", true);
if (data != null)
{
@@ -381,8 +403,11 @@ public class Jalview
ucs.parseAppletParameter(data);
cs = ucs;
}
-
- System.out.println("colour is " + data);
+ else
+ {
+ System.out.println("CMD [-color " + data
+ + "] executed successfully!");
+ }
af.changeColour(cs);
}
@@ -392,30 +417,53 @@ public class Jalview
{
af.parseFeaturesFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD groups[-" + data
+ + "] executed successfully!");
}
data = aparser.getValue("features", true);
if (data != null)
{
af.parseFeaturesFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-features " + data
+ + "] executed successfully!");
}
data = aparser.getValue("annotations", true);
if (data != null)
{
af.loadJalviewDataFile(data, null, null, null);
- System.out.println("Added " + data);
+ // System.out.println("Added " + data);
+ System.out.println("CMD [-annotations " + data
+ + "] executed successfully!");
}
// set or clear the sortbytree flag.
if (aparser.contains("sortbytree"))
{
af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
+ {
+ System.out.println("CMD [-sortbytree] executed successfully!");
+ }
+ }
+ if (aparser.contains("no-annotation"))
+ {
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
+ {
+ System.out.println("CMD no-annotation executed successfully!");
+ }
}
if (aparser.contains("nosortbytree"))
{
af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
+ {
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
+ }
}
data = aparser.getValue("tree", true);
if (data != null)
@@ -423,13 +471,14 @@ public class Jalview
jalview.io.NewickFile fin = null;
try
{
+ System.out.println("CMD [-tree " + data
+ + "] executed successfully!");
fin = new jalview.io.NewickFile(data,
jalview.io.AppletFormatAdapter.checkProtocol(data));
if (fin != null)
{
af.getViewport().setCurrentTree(
af.ShowNewickTree(fin, data).getTree());
- System.out.println("Added tree " + data);
}
} catch (IOException ex)
{
@@ -446,6 +495,7 @@ public class Jalview
{
FeatureFetcher ff = startFeatureFetching(getFeatures);
if (ff != null)
+ {
while (!ff.allFinished() || af.operationInProgress())
{
// wait around until fetching is finished.
@@ -457,6 +507,7 @@ public class Jalview
}
}
+ }
getFeatures = null; // have retrieved features - forget them now.
}
if (groovyscript != null)
@@ -466,8 +517,10 @@ public class Jalview
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, af });
+ executeGroovyScript(groovyscript, new Object[] { desktop, af });
+
+ System.out.println("CMD groovy[" + groovyscript
+ + "] executed successfully!");
}
else
{
@@ -490,6 +543,22 @@ public class Jalview
System.out.println("Creating PNG image: " + file);
continue;
}
+ else if (format.equalsIgnoreCase("svg"))
+ {
+ File imageFile = new java.io.File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ System.out.println("Creating SVG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("html"))
+ {
+ File imageFile = new java.io.File(file);
+ imageName = imageFile.getName();
+ new HtmlSvgOutput(new java.io.File(file), af.alignPanel);
+ System.out.println("Creating HTML image: " + file);
+ continue;
+ }
else if (format.equalsIgnoreCase("imgMap"))
{
af.createImageMap(new java.io.File(file), imageName);
@@ -498,8 +567,10 @@ public class Jalview
}
else if (format.equalsIgnoreCase("eps"))
{
- System.out.println("Creating EPS file: " + file);
- af.createEPS(new java.io.File(file));
+ File outputFile = new java.io.File(file);
+ System.out.println("Creating EPS file: "
+ + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
continue;
}
@@ -526,15 +597,9 @@ public class Jalview
// We'll only open the default file if the desktop is visible.
// And the user
// ////////////////////
-
-
-
-
-
-
if (!headless && file == null && vamsasImport == null
- && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && protein == true)
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
file = jalview.bin.Cache.getDefault(
"STARTUP_FILE",
@@ -587,8 +652,8 @@ public class Jalview
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[]
- { desktop, startUpAlframe });
+ executeGroovyScript(groovyscript, new Object[] { desktop,
+ startUpAlframe });
}
else
{
@@ -607,8 +672,49 @@ public class Jalview
desktop.setInBatchMode(false);
}
}
-
-
+
+ private static void showUsage()
+ {
+ System.out
+ .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ + "-nodisplay\tRun Jalview without User Interface.\n"
+ + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+ + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
+ + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+ + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
+ + "-features FILE\tUse the given file to mark features on the alignment.\n"
+ + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+ + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+ + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+ + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
+ + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+ + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ + "-png FILE\tCreate PNG image FILE from alignment.\n"
+ + "-svg FILE\tCreate SVG image FILE from alignment.\n"
+ + "-html FILE\tCreate HTML file from alignment.\n"
+ + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ + "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ + "-noquestionnaire\tTurn off questionnaire check.\n"
+ + "-nousagestats\tTurn off google analytics tracking for this session.\n"
+ + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
+ // +
+ // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
+ + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
+ + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
+ + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
+ + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+ + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+ // +
+ // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
+ // + "-vses vamsas-session\tJoin session with given URN\n"
+ + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ }
+
private static void startUsageStats(final Desktop desktop)
{
/**
@@ -626,7 +732,7 @@ public class Jalview
public void run()
{
Cache.log
- .info("Initialising googletracker for usage stats.");
+ .debug("Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
Cache.log.debug("Tracking enabled.");
}
@@ -634,7 +740,7 @@ public class Jalview
{
public void run()
{
- Cache.log.info("Not enabling Google Tracking.");
+ Cache.log.debug("Not enabling Google Tracking.");
}
}, null, true);
desktop.addDialogThread(prompter);
@@ -752,17 +858,16 @@ public class Jalview
* = new Binding(); binding.setVariable("input", "world");
* gse.run("hello.groovy", binding);
*/
- Class[] bspec;
+ Class[] bspec;
Object[] binding;
int blen = ((jalviewContext[0] == null) ? 0 : 1)
+ ((jalviewContext[1] == null) ? 0 : 1);
- String cnames[] = new String[]
- { "Jalview", "currentAlFrame" };
+ String cnames[] = new String[] { "Jalview", "currentAlFrame" };
bspec = new Class[blen * 2];
binding = new Object[blen * 2];
blen = 0;
ClassLoader cl = null;
- Map vbinding = new Hashtable();
+ Map vbinding = new HashMap();
for (int jc = 0; jc < jalviewContext.length; jc++)
{
if (jalviewContext[jc] != null)
@@ -779,8 +884,8 @@ public class Jalview
blen++;
}
}
- Class gbindingc = cl.loadClass("groovy.lang.Binding");
- Constructor gbcons;
+ Class gbindingc = cl.loadClass("groovy.lang.Binding");
+ Constructor gbcons;
Object gbinding;
try
{
@@ -790,23 +895,23 @@ public class Jalview
{
// old style binding config - using series of string/object values to
// setVariable.
- gbcons = gbindingc.getConstructor(null);
- gbinding = gbcons.newInstance(null);
+ gbcons = gbindingc.getConstructor();
+ gbinding = gbcons.newInstance();
java.lang.reflect.Method setvar = gbindingc.getMethod(
"setVariable", bspec);
setvar.invoke(gbinding, binding);
}
- ;
- Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
- Constructor gseccons = gsec.getConstructor(new Class[]
- { URL[].class }); // String[].class });
- Object gse = gseccons.newInstance(new Object[]
- { new URL[]
- { sfile } }); // .toString() } });
- java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
- { String.class, gbindingc });
- run.invoke(gse, new Object[]
- { sfile.toString(), gbinding });
+
+ Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+ Constructor gseccons = gsec
+ .getConstructor(new Class[] { URL[].class }); // String[].class
+ // });
+ Object gse = gseccons
+ .newInstance(new Object[] { new URL[] { sfile } }); // .toString()
+ // } });
+ java.lang.reflect.Method run = gsec.getMethod("run", new Class[] {
+ String.class, gbindingc });
+ run.invoke(gse, new Object[] { sfile.toString(), gbinding });
success = true;
} catch (Exception e)
{
@@ -871,6 +976,8 @@ public class Jalview
}
source.addElement(nickname);
}
+ System.out.println("CMD [-dasserver " + data
+ + "] executed successfully!");
} // loop until no more server entries are found.
if (locsources != null && locsources.indexOf('|') > -1)
{
@@ -898,7 +1005,7 @@ public class Jalview
private static FeatureFetcher startFeatureFetching(final Vector dasSources)
{
FeatureFetcher ff = new FeatureFetcher();
- AlignFrame afs[] = Desktop.getAlignframes();
+ AlignFrame afs[] = Desktop.getAlignFrames();
if (afs == null || afs.length == 0)
{
return null;
@@ -909,6 +1016,16 @@ public class Jalview
}
return ff;
}
+
+ public static boolean isHeadlessMode()
+ {
+ String isheadless = System.getProperty("java.awt.headless");
+ if (isheadless != null && isheadless.equalsIgnoreCase("true"))
+ {
+ return true;
+ }
+ return false;
+ }
}
/**
@@ -921,18 +1038,21 @@ public class Jalview
*
*/
-class rnabuttonlistener implements ActionListener{
- public void actionPerformed(ActionEvent arg0) {
- System.out.println("Good idea ! ");
+class rnabuttonlistener implements ActionListener
+{
+ public void actionPerformed(ActionEvent arg0)
+ {
+ System.out.println("Good idea ! ");
- }
+ }
}
-class pbuttonlistener implements ActionListener{
- public void actionPerformed(ActionEvent arg0) {
-
-
- }
+class pbuttonlistener implements ActionListener
+{
+ public void actionPerformed(ActionEvent arg0)
+ {
+
+ }
}
class ArgsParser
@@ -1057,7 +1177,8 @@ class FeatureFetcher
running++;
}
- af.setProgressBar("DAS features being retrieved...", id);
+ af.setProgressBar(MessageManager
+ .getString("status.das_features_being_retrived"), id);
af.featureSettings_actionPerformed(null);
af.featureSettings.fetchDasFeatures(dasSources, true);
af.setProgressBar(null, id);
@@ -1073,7 +1194,5 @@ class FeatureFetcher
{
return queued == 0 && running == 0;
}
-
-
-
-};
+
+}