X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=50e3559272b0c3054c979567f18a092288608304;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=43114d14c36f2223648a74cc0e89b6684bd28261;hpb=8d2724b83aca38ef75d68787cc5939d950467e63;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 43114d1..50e3559 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,25 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 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.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 +36,7 @@ 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 +45,11 @@ import java.security.CodeSource;
import java.security.PermissionCollection;
import java.security.Permissions;
import java.security.Policy;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
-import javax.swing.*;
-
-import jalview.gui.*;
-import jalview.util.Platform;
+import javax.swing.UIManager;
/**
* Main class for Jalview Application
@@ -71,11 +78,6 @@ public class Jalview
}
});
}
- /**
- * Put protein=true for get a protein example
- */
- private static boolean protein=false;
-
/**
* main class for Jalview application
@@ -102,49 +104,31 @@ public class Jalview
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
// anything else!
+
+ final String jabawsUrl = aparser.getValue("jabaws");
+ if (jabawsUrl != null)
+ {
+ try
+ {
+ Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+ } catch (MalformedURLException e)
+ {
+ System.err.println("Invalid jabaws parameter: " + jabawsUrl
+ + " ignored");
+ }
+ }
+
String defs = aparser.getValue("setprop");
while (defs != null)
{
@@ -167,7 +151,8 @@ 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();
@@ -336,7 +321,7 @@ 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);
@@ -413,6 +398,10 @@ public class Jalview
{
af.getViewport().setSortByTree(true);
}
+ if (aparser.contains("no-annotation"))
+ {
+ af.getViewport().setShowAnnotation(false);
+ }
if (aparser.contains("nosortbytree"))
{
af.getViewport().setSortByTree(false);
@@ -446,6 +435,7 @@ public class Jalview
{
FeatureFetcher ff = startFeatureFetching(getFeatures);
if (ff != null)
+ {
while (!ff.allFinished() || af.operationInProgress())
{
// wait around until fetching is finished.
@@ -457,6 +447,7 @@ public class Jalview
}
}
+ }
getFeatures = null; // have retrieved features - forget them now.
}
if (groovyscript != null)
@@ -490,6 +481,22 @@ 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);
@@ -526,15 +533,9 @@ 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",
@@ -607,8 +608,48 @@ 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"
+ + "-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 +667,7 @@ 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 +675,7 @@ 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);
@@ -921,18 +962,21 @@ 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 +1101,7 @@ 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 +1117,5 @@ class FeatureFetcher
{
return queued == 0 && running == 0;
}
-
-
-
+
};