+Adding Groovy Support to Jalview +

David Megginson, David Brownell

+def alf = Jalview.getAlignframes();
+print alf[0].getTitle();
+def alignment = alf[0].viewport.alignment;
+def seq = alignment.getSequenceAt(0);
+
+   ant
+
+mkdir keys
+keytool -genkey -keystore keys/.keystore -keypass alignmentisfun
+-storepass alignmentisfun -alias jalview
+ (you will have to answer some personal questions here)
+ant makedist
+ (should eventually generate a Jalview.jnlp file
+  in ./dist along with a set of signed jars using the jalview
+  key)
+
+ -annotations <Annotations filename>
JALVIEW_ANNOTATION
GRAPH_TYPE	Label	Values
SEQUENCE_REF	seq_name	[startIndex]
SEQUENCE_REF	ALIGNMENT
GROUP_REF	group_name
GROUP_REF	ALIGNMENT
COLOUR	graph_name	colour
+COMBINE	graph_1_name	graph_2_name
+GRAPHLINE	graph_name	value	label	colour
+
ROWPROPERTIES	Row label	centrelabs=true( or false)	showalllabs=true(default is false)	scaletofit=true (default is false)
SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	Sequences
PROPERTIES	Group_name	tab_delimited_key_value_pairs
+
#Comment lines follow the hash symbol
+JALVIEW_ANNOTATION
+SEQUENCE_REF	FER1_MESCR	5
+BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+LINE_GRAPH	Green Values	1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
+LINE_GRAPH	Red Values	2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
+BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
+NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
+COLOUR	Bar Graph 2	blue
+COLOUR	Red Values	255,0,0
+COLOUR	Green Values	green
+COLOUR	Purple Letters	151,52,228
+COMBINE	Green Values	Red Values
+GRAPHLINE	Red Values	2.6	threshold	black
+
+SEQUENCE_GROUP Group_A 30 50 *
+SEQUENCE_GROUP Group_B 1 351 2-5
+SEQUENCE_GROUP Group_C 12 14 -1 seq1	seq2	seq3
+PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false	colourText=false textCol1=black textCol2=black textColThreshold=0
+PROPERTIES Group_B outlineColour=red
+PROPERTIES Group_C colour=Clustal
+
javaws http://www.jalview.org/webstart/jalview.jnlp -open
+ yourFileName
java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] 
+ -features <Features filename>
Feature label	Feature Colour
+<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]]
+
+description	sequenceId	sequenceIndex	start	end	featureType	score (optional)
startgroup	groupname
endgroup	groupname
+domain	red
+metal ion-binding site	00ff00
+transit peptide	0,105,215
+chain	225,105,0
+modified residue	105,225,35
+signal peptide	0,155,165
+helix	ff0000
+strand	00ff00
+coil	cccccc
+Your Own description here	FER_CAPAA	-1	3	93	domain
+Your Own description here	FER_CAPAN	-1	48	144	chain
+Your Own description here	FER_CAPAN	-1	50	140	domain
+Your Own description here	FER_CAPAN	-1	136	136	modified residue
+Your Own description here	FER1_LYCES	-1	1	47	transit peptide
+Your Own description here	Q93XJ9_SOLTU	-1	1	48	signal peptide
+Your Own description here	Q93XJ9_SOLTU	-1	49	144	chain
+startgroup	secondarystucture
+PDB secondary structure annotation	FER1_SPIOL	-1	52	59	strand
+PDB secondary structure annotation	FER1_SPIOL	-1	74	80	helix
+endgroup	secondarystructure
+
jalview.gui.Desktop
+def alf = Jalview.getAlignframes();
+print alf[0].getTitle();
+def alignment = alf[0].viewport.alignment;
+def seq = alignment.getSequenceAt(0);
+
+  >ID/1-10
+  AACDEAAFEA
+
 1GAQ:A
>P1;Q93Z60_ARATH
+sequence:Q93Z60_ARATH:1:.:118:.:.
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSD------QSFLD-D-------------
+---------------------*
+>P1;PDB|1FER|_
+structureX:1FER:1:.:105:.:.
+----------------------------------------------------AFVVTDNCIKCKY---TDCV
+EV-CPVDCFY----EGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEK
+KDPLPDAEDWDGVKGKLQHLE*
+
>P1;Primary_Sequence_ID
+sequence or structureX:pdb-reference if
+  available:start residue:start chain code:end
+  residue:end chain code:. description text
+<jnlp spec="1.0+" codebase="http://www.jalview.org/webstart/" href="http://www.jalview.org/webstart/jalview.jnlp">
+  <information>
+    <title>Jalview</title>
+    <vendor>The Barton Group</vendor>
+    <homepage href="http://www.jalview.org"/>
+    <description>Jalview Multiple Alignment Editor</description>
+    <description kind="short">Jalview</description>
+    <icon href="http://www.jalview.org/webstart/logo_big.gif" kind="default"/>
+    <association extensions="fa" mime-type="application-x/ext-file"/>
+    <association extensions="fasta" mime-type="application-x/ext-file"/>
+    <association extensions="fastq" mime-type="application-x/ext-file"/>
+    <association extensions="blc" mime-type="application-x/ext-file"/>
+    <association extensions="msf" mime-type="application-x/ext-file"/>
+    <association extensions="pfam" mime-type="application-x/ext-file"/>
+    <association extensions="aln" mime-type="application-x/ext-file"/>
+    <association extensions="pir" mime-type="application-x/ext-file"/>
+    <offline-allowed/>
+  </information>
+  <security>
+    <all-permissions/>
+  </security>
+  <resources>
+  <!-- the additional memory parameters are here -->
+  <j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/>
+    <jar href="jalview.jar"/>
+		<jar href="JGoogleAnalytics_0.2.jar"/>
+		<jar href="Jmol-11.0.2.jar"/>
+		<jar href="activation.jar"/>
+		<jar href="axis.jar"/>
+		<jar href="castor-1.1-cycle-xml.jar"/>
+		<jar href="commons-discovery.jar"/>
+		<jar href="commons-logging.jar"/>
+		<jar href="jaxrpc.jar"/>
+		<jar href="jhall.jar"/>
+		<jar href="log4j-1.2.8.jar"/>
+		<jar href="mail.jar"/>
+		<jar href="regex.jar"/>
+		<jar href="saaj.jar"/>
+		<jar href="vamsas-client.jar"/>
+		<jar href="wsdl4j.jar"/>
+		<jar href="xercesImpl.jar"/>
+		<jar href="xml-apis.jar"/>
+		<property name="jalview.version" value="2.4.0.b2"/>
+  </resources>
+  <application-desc main-class="jalview.bin.Jalview"/>
+</jnlp>
+
+<j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/>
+
+file://<full path to file>
+
+lax.nl.java.option.java.heap.size.max=1000m
+lax.nl.java.option.java.heap.size.initial=500m
+
+<key&ht;VMOptions</key&ht;
+<array>
+! <string>-Xms2M</string>
+! <string>-Xmx64M</string>
+</array>
+
+<string>-Xms500M</string>
+<string>-Xmx1000M</string>
+
ILVCAGMFYWHKREQDNSTPBZX-
+XXXXXXXXXXX·······X···XX Hydrophobic
+········XXXXXXXXXX·XXXXX Polar
+··XXXX·········XXXXX··XX Small
+···················X··XX Proline
+····XX···········X····XX Tiny
+XXX···················XX Aliphatic
+·······XXXX···········XX Aromatic
+··········XXX·········XX Positive
+·············X·X······XX Negative
+··········XXXX·X······XX Charged
saxon.jar
/lib
extensions/saxon651.jar
/lib
+ ..
+   ant/                  The Ant Plug-in
+   build/                The Jalopy build system
+   console/
+   docu/                 All documentation sources
+   eclipse/              The Eclipse Plug-in
+   jbuilder/             The JBuilder Plug-in
+   jdeveloper/           The JDeveloper Plug-in
+   jedit/                The jEdit Plug-in
+   main/                 The core Jalopy sources
+   netbeans/             The NetBeans/Sun ONE Studio Plug-in
+
/build
build.properties
file:///G:/XML/docbook-xsl-1.62.4
<modulename>
<libraryname>
target
target
-projecthelp
tmp~/dist
tmp~
// text
//
+// [PENDING] this should be part of the ErrorManager
+
/* text */
/*
*/
+/* public int getSubregionStartOffset(int line, int subregion)
+{
+	ChunkCache.LineInfo[] lineInfos = chunkCache.getLineInfosForPhysicalLine(line);
+	return buffer.getLineStartOffset(lineInfos[subregion].physicalLine)
+		+ lineInfos[subregion].offset;
+} */
+
/** text */
/**
*/
+/**
+ * A scroll listener will be notified when the text area is scrolled, either
+ * horizontally or vertically.
+ *
+ * @author Slava Pestov
+ * @since jEdit 3.2pre2
+ */
+
//~ text
//~
+//~ Inner classes .......................................
+
//J[directive]
//J[-|+]
+//J-
+    if {condition()) return value;
+//J+
+
//J-
//J+
//J-
//J+
//J+
+/* Multi-line
+* comment.
+* end.
+*/
+
+/* Multi-line
+ * comment.
+ * end.
+ */
+
([a-zA-Z_][a-zA-Z0-9_.])+
/usr/projects/test/MyFile.java
MyFile.java
$([a-zA-Z_][a-zA-Z0-9_.]+)$
+//==============================================================================
+// file :       $fileName$
+// project:     $project$
+//
+// last change: date:       $Date$
+//              by:         $Author$
+//              revision:   $Revision$
+//------------------------------------------------------------------------------
+// copyright:   BSJT Software License (see class documentation)
+//==============================================================================
+
+//==============================================================================
+// file :       Byte.java
+// project:     bsjt-rt
+//
+// last change: date:       $Date$
+//              by:         $Author$
+//              revision:   $Revision$
+//------------------------------------------------------------------------------
+// copyright:   BSJT Software License (see class documentation)
+//==============================================================================
+
+I newly installed jalopy-1.0b9 on Windows NT with German locales, Sun JDK 1.3.1_05.
+I upgraded property file from jalopy-1.0b7 via Import/Export.
+
+When starting the jalopy settings dialog, I always have problems
+when I am on the "Sorting" panel. No entries are shown. Maybe
+this is a similar problem.
+
+I tried with different files. Always the same result.
+
+Using the Ant task (0.3.3 with Ant 1.4.1), I get a stack trace as attached. I attached
+my code convention also.
+
+[jalopy] Jalopy Java Source Code Formatter 1.0b9
+[jalopy] Format 1 source file
+[jalopy] X:\beans\booking\BookingService.java:0:0:
+Parse
+[jalopy] X:\beans\booking\BookingService.java:0:0:parsing took 170
+[jalopy] X:\beans\booking\BookingService.java:0:0:transform
+[jalopy] X:\beans\booking\BookingService.java:0:0:
+java.lang.NullPointerException
+[jalopy] java.lang.NullPointerException
+at de.hunsicker.jalopy.lang.Transformation.addSiblings(Transformation.java:167)
+at de.hunsicker.jalopy.lang.Transformation.sortDeclarations(Transformation.java:534)
+at de.hunsicker.jalopy.lang.Transformation.sort(Transformation.java:104)
+at de.hunsicker.jalopy.lang.Transformation.apply(Transformation.java:64)
+at de.hunsicker.jalopy.lang.JavaRecognizer.transform(JavaRecognizer.java:451)
+at de.hunsicker.jalopy.lang.JavaRecognizer.getParseTree(Java Recognizer.java:173)
+
+/*
+ *                 Sun Public License Notice
+ *
+ * The contents of this file are subject to the Sun Public License
+ * Version 1.0 (the "License"). You may not use this file except in
+ * compliance with the License. A copy of the License is available at
+ * http://www.sun.com/
+ *
+ * The Original Code is NetBeans. The Initial Developer of the Original
+ * Code is Sun Microsystems, Inc. Portions Copyright 1997-2000 Sun
+ * Microsystems, Inc. All Rights Reserved.
+ */
+
UTF-8
operators
@throws
@throws
@throws
user.name
synchronized
jalopy.sh
preferences.sh
org.eclipse.swt.SWTException: invalid thread access
.XML
.XML
/bin
/lib
/bin
/lib
@todo
%
JEditorPane
textarea-2.2.3.jar
--force
l
abstract
assert
n
new String[0]
do-while
@link
/lib
if (obj.getClass() == (byte.class))
try
catch
IllegalArgumentException
.jars
extends
implements
throws
.jar
.jar
instanceof
Configuration.debug()
.XML
.nbm
plugin.xml
IllegalArgumentException
Category
Priority
AbstractPlugin.java
threads
NumberComboBoxEditor.java
loglevel
.XML
style
Jalopy.java
util.concurrent
AbstractPlugin.java
SwingWorker.java
SwingWorker.java
0
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import java.util.ArrayList;
+import java.util.List;
+
asterix
+import java.util.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public void severalParameters(String one, int two, String three,
+    StringObject four, AnotherObject five) {
+...
+}
+
+vector.add(new AppServerReference(
+        "RemoteApplicationManager",
+        poa.create_reference_with_id("RemoteApplicationManager".getBytes(),
+            RemoteApplicationManagerHelper.id())));
+
+doublette[InteressentenPflegeController.GEBURTSDATUM] = versichertenResultSetRow[i].field[0]
+    .substring(0, 2) + "."
+    + versichertenResultSetRow[i].field[0].substring(2, 4) + "."
+    + versichertenResultSetRow[i].field[0].substring(4, 6);
+
+public void severalParameters(String one, int two, String three,
+                              StringObject four, AnotherObject five) {
+    ...
+}
+
+this.add(lbPunktzahl,
+         new GridBagLayout(0, 1, 2, 1, 0.0, 0.0,
+                           GribBagConstraints.WEST,
+                           GribBagConstraints.NONE,
+                           new Insets(0, GribBagConstraints.WEST,
+                                      GribBagConstraints.WEST,
+                                      GribBagConstraints.WEST), 0, 0));
+
+doublette[Controller.GEBURTSDATUM] = versichertenResultSetRow[i].field[0]
+                                     .substring(0, 2) + "."
+                                     + versichertenResultSetRow[i].field[0]
+                                       .substring(2, 4)
+                                     + "."
+                                     + versichertenResultSetRow[i].field[0]
+                                       .substring(4, 6);
+
+public class Preferences
+{
+->private Preferences()
+->{
+->}
+
+->public static void main(String[] argv)
+->{
+->->de.hunsicker.jalopy.swing.PreferencesDialog.main(argv);
+->}
+}
+
+public class Preferences
+{
+--->private Preferences()
+--->{
+--->}
+
+--->public static void main(String[] argv)
+--->{
+--->--->de.hunsicker.jalopy.swing.PreferencesDialog.main(argv);
+--->}
+}
+
+----->public class Preferences
+----->{
+----->    private Preferences()
+----->    {
+----->    }
+
+----->    public static void main(String[] argv)
+----->    {
+----->        de.hunsicker.jalopy.swing.PreferencesDialog.main(argv);
+----->    }
+----->}
+
+if ((condition1 && condition2)
+    ->|| (condition3 && condition4)
+    ->|| !(condition5 && condition6)) {
+    doSomethingAboutIt();
+}
+
+if ((condition1 && condition2)
+    --->|| (condition3 && condition4)
+    --->|| !(condition5 && condition6)) {
+    doSomethingAboutIt();
+}
+
+new String[] {
+    "Sunday",-->// Sunday
+    "Monday",-->// Monday
+    "Tuesday",-->// Tuesday
+    "Wednesday",-->// Wednesday
+    "Thursday",-->// Thursday
+    "Friday",-->// Friday
+    "Saturday"-->// Saturday
+}
+
extends
+public interface Channel
+------>extends Puttable, Takable
+{
+    ...
+}
+
implements
+public class SynchronizedBoolean
+------->implements Comparable, Cloneable
+{
+    ...
+}
+
throws
+private static final File getDestinationFile(File dest, String packageName,
+                                             String filename)
+-->throws IOException, FooException
+{
+    ...
+}
+
+switch (prio)
+{
+case Priority.ERROR_INT :
+case Priority.FATAL_INT :
+    color = Color.red;
+    break;
+
+case Priority.WARN_INT :
+    color = Color.blue;
+    break;
+
+default:
+    color = Color.black;
+    break;
+}
+
+switch (prio)
+{
+--->case Priority.ERROR_INT :
+--->case Priority.FATAL_INT :
+--->    color = Color.red;
+--->    break;
+
+--->case Priority.WARN_INT :
+--->    color = Color.blue;
+--->    break;
+
+--->default:
+--->    color = Color.black;
+--->    break;
+}
+
+// advance to the first CLASS_DEF or INTERFACE_DEF
+LOOP:
+        for (AST child = tree.getFirstChild();
+             child != null;
+             child = child.getNextSibling())
+        {
+            switch (child.getType())
+            {
+                case JavaTokenTypes.CLASS_DEF :
+                case JavaTokenTypes.INTERFACE_DEF :
+                    next = child;
+                    break LOOP;
+                default :
+                    break;
+            }
+        }
+
+        // advance to the first CLASS_DEF or INTERFACE_DEF
+        LOOP:
+        for (AST child = tree.getFirstChild();
+             child != null;
+             child = child.getNextSibling())
+        {
+            switch (child.getType()) {
+                case JavaTokenTypes.CLASS_DEF :
+                case JavaTokenTypes.INTERFACE_DEF :
+                    next = child;
+                    break LOOP;
+
+                default :
+                    break;
+            }
+        }
+
+    public static Printer create(AST node)
+    {
+
+        /*
+        if (node == null)
+        {
+            return new NullPrinter();
+        }
+        */
+        return create(node.getType());
+    }
+
+    public static Printer create(AST node)
+    {
+
+/*
+        if (node == null)
+        {
+            return new NullPrinter();
+        }
+*/
+        return create(node.getType());
+    }
+
+String text = "text";
+int a = -1;
+History.Entry entry = new History.Entry(text);
+
+String        text = "text";
+int           a = -1;
+History.Entry entry = new History.Entry(text);
+
+String text         = "text";
+int a               = -1;
+History.Entry entry = new History.Entry(text);
+
+String        text  = "text";
+int           a     = -1;
+History.Entry entry = new History.Entry(text);
+
+public static File create(final File file,
+                          File directory,
+                          int backupLevel)
+{
+    ...
+}
+
+public static File create(final File file,
+                          File       directory,
+                          int        backupLevel)
+{
+    ...
+}
+
+Fachschluesselerzeugung.createService()
+.getNeuerFachschluesselServiceService(
+    FachschluesselerzeugungService.FACHSCHLUESSEL_KZ_INTERESSENT);
+
+Fachschluesselerzeugung.createService()
+                       .getNeuerFachschluesselServiceService(
+                            FachschluesselerzeugungService.FACHSCHLUESSEL_KZ_INTERESSENT);
+
+        alpha = (aLongBooleanExpression) ? beta    |
+        : gamma;                                   |
+
+        alpha = (aLongBooleanExpression) ? beta    |
+                : gamma;                           |
+
+        alpha = (aLongBooleanExpression) ? beta    |
+                                         : gamma;  |
+
if
for
while
do-while
+if ((condition1 && condition2)
+    || (condition3 && condition4)
+    || !(condition5 && condition6)) { // BAD WRAPS
+    doSomethingAboutIt();             // MAKE THIS LINE EASY TO MISS
+}
+
+if ((condition1 && condition2)
+        || (condition3 && condition4)
+        || !(condition5 && condition6)) {
+    doSomethingAboutIt();
+}
+
+String comma = spaceAfterComma
+               --->? COMMA_SPACE
+               --->: COMMA;
+
Object
equals
hashCode
equals
equals
hashCode
toString
nulls
wait
+private static final List _favorableTypes = new ArrayList(20); // List of <String>
+
finally
finally
finally
+Writer writer = null;
+
+try
+{
+    writer = new BufferedWriter(new FileWriter(file));
+    write.write(data);
+}
+catch (IOException ex)
+{
+    System.err.println("file could not be written -- " + file);
+}
+finally
+{
+}
+
Writer
finally
/* NOI18N */
/* NOI18N */
+FileDialog dialog = new FileDialog(this,
+    ResourceBundle.getBundle(BUNDLE_NAME)
+    .getString("BTN_SAVE_AS", FileDialog.SAVE); //$NON-NLS-1$
+
+FileDialog dialog =
+    new FileDialog(this,
+                   ResourceBundle.getBundle(BUNDLE_NAME).
+                                  getString("BTN_SAVE_AS",
+                   FileDialog.SAVE); //$NON-NLS-1$
+
+FileDialog dialog =
+    new FileDialog(this,
+                   ResourceBundle.getBundle(BUNDLE_NAME).
+                                  getString("BTN_SAVE_AS" /* NOI18N */),
+                   FileDialog.SAVE);
+
<p>
<li>
<dd>
<dt>
<dir>
<
>
&
@
+/**
+ * @author <a href="mailto:first.last@company.com">first.last@company.com</a>
+ */
+
+/**
+ * @author <a href="mailto:first.last@company.com">first.last&064;company.com</a>
+ */
+
@throws
@throws
@throws
IOException
FileNotFoundException
+/**
+ * What history policy should be used?
+ */
+private History.Policy _historyPolicy = History.Policy.DISABLED;
+
+/** What history policy should be used? */
+private History.Policy _historyPolicy = History.Policy.DISABLED;
+
@author
@deprecated
@exception
@param
@return
@see
@serial
@serialData
@serialField
@since
@throws
@todo
@version
@[a-zA-Z]+
@exclude
@docRoot
@inheritDoc
@link
@linkPlain
@value
@[a-zA-Z]+
@mylink
ERROR
DEBUG
+int result = 12 + 4 % 3 * 7 / 8;
+
+int result = 12 + ((4 % 3 * 7) / 8);
+
java.io.Serializable
java.io.Externalizable
+logger.debug("some message: " + someVar);
+
+if (logger.isDebugEnabled()) {
+    logger.debug("some message: " + someVar);
+}
+
+int[] a;
+
+int a[];
+
history.dat
/bin
.jar
+java Preferences
+
1
8
+<?xml version="1.0" ?>
+<project name="myProject" default="format" basedir="." >
+
+  <property name="dir.jalopy" value="/mystuff/jalopy/bin" />
+  <property name="dir.lib" value="${basedir}/ext/lib" />
+  <property name="dir.compile" value="${basedir}/tmp~/build/classes" />
+  <property name="dir.src.java" value="${basedir}/src/java" />
+
+  <!-- ==================================================================== -->
+  <!-- Defines the Jalopy task                                              -->
+  <!-- ==================================================================== -->
+  <taskdef name="jalopy"
+           classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
+    <!--
+
+      we did not copy the needed .jars into the /lib directory of Ant in order
+      to avoid possible classpath issues, so we have to specify a lookup
+      classpath here
+
+      -->
+    <classpath>
+      <fileset dir="${dir.jalopy}">
+        <include name="*.jar" />
+      </fileset>
+    </classpath>
+  </taskdef>
+
+
+  <!-- ==================================================================== -->
+  <!-- Defines the project classpath                                        -->
+  <!-- ==================================================================== -->
+  <path id="project.classpath" >
+
+    <!-- our compilation directory -->
+    <pathelement location="${dir.compile}" />
+
+    <!-- needed 3rd party libraries -->
+    <fileset dir="${dir.lib}" >
+      <include name="**/*.jar" />
+    </fileset>
+  </path>
+
+
+  <!-- ==================================================================== -->
+  <!-- Compiles the project sources                                         -->
+  <!-- ==================================================================== -->
+  <target name="compile"
+          depends="init">
+    <javac destdir="${dir.compile}"
+           fork="true">
+      <classpath refid="project.classpath" />
+      <src path="${dir.src.java}" />
+    </javac>
+  </target>
+
+
+  <!-- ==================================================================== -->
+  <!-- Formats all source files                                             -->
+  <!-- ==================================================================== -->
+  <target name="format" depends="compile">
+
+    <!--
+
+      Invokes Jalopy as follows:
+
+      - All formatted files will have unix fileformat (\n)
+      - Load your code convention from the given url
+      - Override the convention to use the file history feature
+      - Override the convention to use alder32 checksums of files for history testing
+      - Override the convention to use loglevel "info"
+      - Override the convention to use 2 threads
+      - The import optimization feature will work (if enabled in the active
+        convention), because a classpath reference is specified
+
+        Don't forget to setup an include pattern as Jalopy truly expects
+        valid Java source files as input!
+
+      -->
+    <jalopy fileformat="unix"
+            convention="http://www.foo.com/myConvention.xml"
+            history="file"
+            historymethod="adler32"
+            loglevel="info"
+            threads="2"
+            classpathref="project.classpath">
+      <fileset dir="${dir.src.java}">
+        <include name="**/*.java" />
+      </fileset>
+    </jalopy>
+  </target>
+</project>
+
.zip
.tar
<INST_DIR>
/bin
/docs
/lib
+..
+  bin/       contains wrapper scripts for different platforms
+  docs/      contains the documentation
+  lib/       contains all necessary libraries
+
+<taskdef name="jalopy"
+         classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
+  <classpath>
+    <fileset dir="<INST_DIR>/lib">
+      <include name="*.jar" />
+    </fileset>
+  </classpath>
+</taskdef>
+
/lib
aelfred-xxx.jar
/lib
+jalopy [-options] args...
+
+java Jalopy [-options] args...
+
+java -jar jalopy-<version>.jar [-options] args...
+
args
args
+-c, --convention=FILE   use FILE as code convention file
+    --disclaimer        print software disclaimer
+-d, --dest=DIR          use DIR as base output directory
+-e, --encoding=WORD     assume WORD as encoding of input files where WORD
+                        describes one of the JDK supported encodings
+                        (if omitted, the platform default is used)
+-f, --format=WORD       use WORD as output file format where WORD can be
+                        either UNIX, DOS, MAC, AUTO (the default) or DEFAULT
+                        (all case-insensitive)
+    --force             force formatting even if file up-to-date
+-h, --help              display this help
+    --nobackup          don't keep backup files
+-r, --recursive{=NUM}   recurse into directories, up to NUM levels
+                        if NUM is omitted, recurses indefinitely
+-t, --thread=NUM        use NUM processing threads
+-v, --version           print product version and exit
+
+jalopy -r myDirectory
+
myDirectory
+jalopy -d /directory -f DOS
+myFile1.java myFile2.java
+
myFile1.java
myFile2.java
/directory
+jalopy -r 3 -d /directory ^A.*java
+
/tmp
+type f:\test\in.java | jalopy > out.java
+
f:\test\in.java
out.java
.zip
.tar
<INST_DIR>
/bin
/docs
/lib
+..
+  bin/       contains wrapper scripts for different platforms
+  docs/      contains the documentation
+  lib/       contains all necessary libraries
+
/bin
-jar
-jar
.jar
+export CLASSPATH=${CLASSPATH}:<INST_DIR>/lib/jalopy-console-<version>.jar
+
+set CLASSPATH=%CLASSPATH%;<INST_DIR>\lib\jalopy-console-<version>.jar
+
.zip
.tar
<INST_DIR>
/de.hunsicker.jalopy.plugin.eclipse_version
/docs
+..
+  de.hunsicker.jalopy.plugin.eclipse_version/    contains the Plug-in files
+  docs/                                          contains the documentation
+
de.hunsicker.jalopy.plugin.eclipse_version
.zip
.tar
<INST_DIR>
/docs
/lib
+..
+  docs/      contains documentation
+  lib/       contains all necessary libraries
+
/lib/ext
<INST_DIR>/lib
/lib/ext
$HOME/.jalopy
.zip
.tar
<INST_DIR>
/docs
/lib
+..
+  docs/      contains the documentation
+  lib/       contains all necessary libraries
+
<INST_DIR>/lib
/jdev/lib/ext
.zip
.tar
<INST_DIR>
/docs
/lib
+..
+  docs/      contains the documentation
+  lib/       contains all necessary libraries
+
.jar
<INST_DIR>/lib
/jars
.zip
.tar
<INST_DIR>
/docs
/lib
+..
+  docs/      contains the documentation
+  lib/       contains all necessary libraries
+
.nbm
<INST_DIR>/lib
+if (!isDone)
+{
+    doSomething();
+}
+else
+{
+    System.err.println("Finished");
+}
+
+if (!isDone) {
+    doSomething();
+} else {
+    System.err.println("Finished");
+}
+
+if (!isDone)
+  {
+    doSomething();
+  }
+else
+  {
+    System.err.println("Finished");
+  }
+
throws
extends
implements
throws
if
for
while
do-while
while
+while (!isDone)
+    doSomething();
+
+while (!isDone)
+{
+    doSomething();
+}
+
if
for
while
do-while
+for (int i = 0; i < 100; i++)
+{
+    sum += value[i];
+}
+
+for (int i = 0; i < 100; i++)
+    sum += value[i];
+
+if (in != null)
+{
+    try
+    {
+        in.close();
+    }
+    catch (IOException ignored)
+    {
+    }
+}
+
+if (in != null)
+{
+    try
+    {
+        in.close();
+    }
+    catch (IOException ignored)
+    {
+        ;
+    }
+}
+
+if (in != null)
+{
+    try
+    {
+        in.close();
+    }
+    catch (IOException ignored) {}
+}
+
package de.hunsicker.jalopy.printer;
+<--
+<--
+<--
+import antlr.collections.AST;
+
+import de.hunsicker.jalopy.parser.JavaAST;
+import de.hunsicker.jalopy.parser.JavaTokenTypes;
+
+...
+
package de.hunsicker.jalopy.printer;
+
+import antlr.collections.AST;
+
+import de.hunsicker.jalopy.parser.JavaAST;
+import de.hunsicker.jalopy.parser.JavaTokenTypes;
+<--
+<--
+<--
+<--
+public class Printer
+{
+    ...
+}
+
class One
+{
+    ...
+}
+<--
+<--
+class Two
+{
+    ...
+}
+
interface One
+{
+    ...
+}
+<--
+<--
+<--
+interface Two
+{
+    ...
+}
+
public static Printer getInstance()
+{
+    return INSTANCE;
+}
+<--
+<--
+<--
+public void print(AST node, ASTWriter out)
+           throws IOException
+{
+    ...
+}
+
AST type = null;
+<--
+<--
+switch (next.getType())
+{
+    case JavaTokenTypes.LPAREN :
+        type = PrinterUtils.advanceToFirstNonParen(next);
+        break;
+    default :
+        type = next;
+        break;
+}
+<--
+<--
+AST ident = type.getFirstChild();
+
switch (next.getType())
+{
+<--
+<--
+<--
+    case JavaTokenTypes.LPAREN :
+        type = PrinterUtils.advanceToFirstNonParen(next);
+        break;
+<--
+<--
+<--
+    default :
+        type = next;
+        break;
+}
+
switch (next.getType())
+{
+    case JavaTokenTypes.LPAREN :
+        type = PrinterUtils.advanceToFirstNonParen(next);
+<--
+<--
+        break;
+
+    default :
+        type = next;
+<--
+<--
+        break;
+}
+
public void foo()
+{
+<--
+    if (condition())
+    {
+<--
+        if (anotherCondition())
+        {
+            doSomething();
+        }
+    }
+}
+
public void foo()
+{
+    if (condition())
+    {
+        if (anotherCondition())
+        {
+            doSomething();
+        }
+    }
+}
+
public void foo()
+{
+    if (condititon())
+    {
+        if (anotherCondition())
+        {
+            doSomething();
+<--
+        }
+<--
+    }
+<--
+}
+
aMVString = new MultiValueString("abc");
+<--
+System.out.println("MV = "+aMVString);
+<--
+System.out.println("MV0 = "+aMVString.extract(0));
+System.out.println("MV1 = "+aMVString.extract(1));
+System.out.println("MV2 = "+aMVString.extract(2));
+System.out.println("");
+
+String        text  = "text";
+int           a     = -1;
+
+// create a new entry
+History.Entry entry = new History.Entry(text);
+
+String text  = "text";
+int    a     = -1;
+
+// create a new entry
+History.Entry entry = new History.Entry(text);
+
+//~ Methods ------------------------------------------------------------------
+
$HOME/.jalopy
$HOME/.jalopy/PROJECT_DIR/preferences.dat
assert
.jal
+class TypePrinter
+    extends AbstractPrinter
+{
+    //~ Instance/static variables ----------------------------------------------
+
+    /** Singleton. */
+    private final static Printer INSTANCE = new TypePrinter();
+
+    //~ Constructors -----------------------------------------------------------
+
+    /**
+     * Creates a new TypePrinter object.
+     */
+    protected TypePrinter()
+    {
+    }
+
+    //~ Methods ----------------------------------------------------------------
+
+    public static Printer getInstance()
+    {
+        return INSTANCE;
+    }
+
+    public void print(AST node, ASTWriter out)
+               throws IOException
+    {
+        AST child = node.getFirstChild();
+        PrinterFactory.create(child).print(child, out);
+    }
+}
+
+public void someMethod()) {
+  ...
+}
+
+public void someMethod ()) {
+  ...
+}
+
+for (Iterator i = pointList.iterator(); i.hasNext();) {
+    ...
+}
+
+for (Iterator i = pointList.iterator (); i.hasNext ();) {
+    ...
+}
+
+while(!isDone)
+    doSomething();
+
+while (!isDone)
+    doSomething();
+
+    String[] values = new String[]{
+        "One", "Two", "Three", "Four", "Five", "Six", "Seven"
+    };
+
+    String[] values = new String[] {
+        "One", "Two", "Three", "Four", "Five", "Six", "Seven"
+    };
+
+for (i = 0; i < 100; i++)
+    sum += value[i];
+
+for (i = 0; i < 100; i++)
+    sum += value [i];
+
+String[] names = (String[])data.toArray(new String[]);
+
+String [] names = (String [])data.toArray(new String []);
+
+switch (character) {
+    case 'A':
+        break;
+}
+
+switch (character) {
+    case 'A' :
+        break;
+}
+
+doSomething (a,b,c,d);
+
+doSomething (a, b, c, d);
+
+for (i=0;i<10;i++) ...
+
+for (i=0; i<10; i++) ...
+
+int line = ((JavaAST)node).getStartLine();
+
+int line = ((JavaAST) node).getStartLine();
+
+while(!isDone) {
+    doSomething();
+}
+
+while(! isDone) {
+    doSomething();
+}
+
+a=(b+c)*d;
+a = (b+c)*d;
+
+if((LA(1)=='/')&&(LA(2)!='*'||(LA(2)=='*'&&LA(3)!='*'))) ...
+
+if((LA(1)=='/') && (LA(2)!='*' || (LA(2)=='*' && LA(3)!='*'))) ...
+
+if((LA(1)=='\n'||LA(1)=='\r')) ...
+
+if((LA(1) == '\n'||LA(1) == '\r')) ...
+
+public static final boolean isUnix()
+{
+    return (getOperatingSystem()&PLAT_UNIX) != 0;
+}
+
+public static final boolean isUnix()
+{
+    return (getOperatingSystem() & PLAT_UNIX) != 0;
+}
+
+a=(b+c)*d;
+
+a=(b + c) * d;
+
+if(((1L<<i)&l)!=0)
+    System.out.print("1");
+
+if(((1L << i)&l)!=0)
+    System.out.print("1");
+
+Object[] items = {"2", "3", "4"};
+
+Object[] items = { "2", "3", "4" };
+
+for (i = 0; i < 100; i++)
+    sum += value[i];
+
+for(i = 0; i < 100; i++)
+    sum += value[ i ];
+
+GridBagLayout layout = new GridBagLayout();
+setLayout(layout);
+
+GridBagLayout layout = new GridBagLayout();
+setLayout( layout );
+
+int line = ((JavaAST)node).getStartLine();
+
+int line = (( JavaAST )node).getStartLine();
+
+                                                            |                  |
+    protected static synchronized File getANewDestinationFile(File dest,       |
+                                                            | String packageName,
+                                                            | String filename) |
+|----------------- the gap ---------------------------|throws IOException      |
+    {                                                       |                  |
+    }                                                       |                  |
+                                                            |                  |
+                                                            60                 79
+
+                                                  |                            |
+    protected static synchronized File getANewDestinationFile(File dest,       |
+                                                  |           String packageName,
+                                                  |           String filename) |
+|----------------- the gap ---------------------------|throws IOException      |
+    {                                             |                            |
+    }                                             |                            |
+                                                  |                            |
+                                                  50                           79
+
+                                                                               |
+appServerReferencesVector.add(new AppServerReference(
+        "RemoteApplicationManager",                                            |
+        poa.create_reference_with_id(         |
+            "RemoteApplicationManager".getBytes(),                             |
+            RemoteApplicationManagerHelper.id())));                            |
+                                                                               |
+
+appServerReferencesVector.add(
+    new AppServerReference(
+        "RemoteApplicationManager",
+        poa.create_reference_with_id(
+            "RemoteApplicationManager".getBytes(),
+            RemoteApplicationManagerHelper.id())));
+
if-else
for
while
do-while
if-else
for
while
do-while
+public void severalParameters(String one,
+                              int two,
+                              String three,
+                              StringObject four,
+                              AnotherObject five) {
+}
+
+public void severalParameters(String one,
+                              int two,
+                              String three,
+                              StringObject four,
+                              AnotherObject five
+) {
+}
+
+appServerReferencesVector.add(
+    new AppServerReference(
+        "RemoteApplicationManager",
+        poa.create_reference_with_id(
+            "RemoteApplicationManager".getBytes(),
+            RemoteApplicationManagerHelper.id()
+        )
+    )
+);
+
+if (
+    "pick".equals(m.getName()) && m.isStatic() && m.isPublic()
+) {
+    pickFound = true;
+}
+else if (
+    "pick".equals(m.getName()) && m.isStatic() && m.isPublic()
+) {
+    pickFound = true;
+}
+
+if (
+    !((bankverbindung instanceof ObjectValue)
+    || (bankverbindung instanceof PrimitiveValue))
+) {
+    throw new RuntimeException();
+}
+
+if (
+    !(
+        (bankverbindung instanceof ObjectValue)
+        || (bankverbindung instanceof TkPrimitiveValue)
+    )
+) {
+    throw new RuntimeException();
+}
+
+this.interessentenNr = new InteressentenNr(
+        Fachschluesselerzeugung.createService()
+        .getNeuerFachschluessel(
+            FachschluesselerzeugungService.FACHSCHLUESSEL_KZ_INTERESSENT
+        )
+    );
+
+this.interessentenNr =
+    new InteressentenNr(
+        Fachschluesselerzeugung.createService()
+        .getNeuerFachschluessel(
+            FachschluesselerzeugungService.FACHSCHLUESSEL_KZ_INTERESSENT
+        )
+    );
+
+if ((condition1 && condition2)
+    || (condition3 && condition4)
+    || !(condition5 && condition6))
+{
+    doSomethingAboutIt();
+}
+
+if ((condition1 && condition2) ||
+    (condition3 && condition4) ||
+    !(condition5 && condition6))
+{
+    doSomethingAboutIt();
+}
+
+public interface Channel extends Puttable, Takable
+{
+    ...
+}
+
+public interface Channel
+    extends Puttable, Takable
+{
+    ...
+}
+
+public interface Channel extends Puttable, Takable
+{
+    ...
+}
+
+public interface Channel extends Puttable,
+                                 Takable
+{
+    ...
+}
+
+public class SynchronizedBoolean implements Comparable, Cloneable
+{
+    ...
+}
+
+public class SynchronizedBoolean
+    implements Comparable, Cloneable
+{
+    ...
+}
+
+public class SynchronizedBoolean implements Comparable, Cloneable
+{
+    ...
+}
+
+public class SynchronizedBoolean implements Comparable,
+                                            Cloneable
+{
+    ...
+}
+
+private File getDestinationFile(File dest, String packageName,
+                                String filename) throws IOException
+{
+    ...
+}
+
+private File getDestinationFile(File dest, String packageName,
+                                String filename)
+                         throws IOException
+{
+    ...
+}
+
+private File getDestinationFile(File dest, String packageName,
+                                String filename)
+                         throws IOException, FooException
+{
+    ...
+}
+
+private File getDestinationFile(File dest, String packageName,
+                                String filename)
+                         throws IOException,
+                                FooException
+{
+    ...
+}
+
+private static final File getDestinationFile(File dest, String packageName,
+                                             String filename)
+    throws IOException,
+          FooException
+{
+    ...
+}
+
+public static File create(File file, File directory, int backupLevel)
+                   throws IOException
+{
+    ...
+}
+
+public static File create(File file,
+                          File directory,
+                          int backupLevel)
+                   throws IOException
+{
+    ...
+}
+
+message.format(ERROR_SOURCE_ADDRESS).param (m_session.getAimName()).send();
+
+message.format(ERROR_SOURCE_ADDRESS)
+       .param (m_session.getAimName())
+       .send();
+
+doSomething();
+_userDatabase.addUser("Name", encryptPassword("password", _secretKey),
+                      "123 fake address");
+doSomethingElse();
+
+doSomething();
+_userDatabase.addUser("Name",
+                      encryptPassword("password",
+                                      _secretKey),
+                      "123 fake address");
+doSomethingElse();
+
+doSomething();
+_userDatabase.addUser("Name",
+                      encryptPassword("password", _secretKey),
+                      "123 fake address");
+doSomethingElse();
+
?
+String comma = spaceAfterComma
+               ? COMMA_SPACE : COMMA;
+
:
+String comma = spaceAfterComma ? COMMA_SPACE
+                               : COMMA;
+
+String comma = spaceAfterComma ? COMMA_SPACE : COMMA;
+
+String comma = spaceAfterComma
+    ? COMMA_SPACE
+    : COMMA;
+
+// advance to the first CLASS_DEF or INTERFACE_DEF
+LOOP:   for (AST child = tree.getFirstChild();
+             child != null;
+             child = child.getNextSibling())
+        {
+            switch (child.getType())
+            {
+                case JavaTokenTypes.CLASS_DEF :
+                case JavaTokenTypes.INTERFACE_DEF :
+                    next = child;
+                    break LOOP;
+
+                default :
+                    break;
+            }
+        }
+
+// advance to the first CLASS_DEF or INTERFACE_DEF
+LOOP:
+        for (AST child = tree.getFirstChild();
+             child != null;
+             child = child.getNextSibling())
+        {
+            switch (child.getType())
+            {
+                case JavaTokenTypes.CLASS_DEF :
+                case JavaTokenTypes.INTERFACE_DEF :
+                    next = child;
+                    break LOOP;
+
+                default :
+                    break;
+            }
+        }
+
extends
+public interface VeryImportantInterface                        |
+    extends LeastImportantInterface, LessImportantInterface,   |
+        ImportantInterface                                     |
+}                                                              |
+    ...                                                        |
+}                                                              |
+
+public interface VeryImportantInterface                        |
+    extends LeastImportantInterface,                           |
+        LessImportantInterface,                                |
+        ImportantInterface                                     |
+}                                                              |
+    ...                                                        |
+}                                                              |
+
implements
+public class ImportantClass                                    |
+    implements ImportantInterface, Serializable, Comparable,   |
+        Cloneable                                              |
+}                                                              |
+    ...                                                        |
+}                                                              |
+
+public class ImportantClass                                    |
+    implements ImportantInterface,                             |
+        Serializable,                                          |
+        Comparable,                                            |
+        Cloneable                                              |
+}                                                              |
+    ...                                                        |
+}                                                              |
+
throws
+private File getDestinationFile(File dest, String packageName, |
+                                String filename)               |
+                         throws IOException, FooException,     |
+                                FooBarException                |
+{                                                              |
+    ...                                                        |
+}                                                              |
+
+private File getDestinationFile(File dest, String packageName, |
+                                String filename)               |
+                         throws IOException,                   |
+                                FooException,                  |
+                                FooBarException                |
+{                                                              |
+    ...                                                        |
+}                                                              |
+
+if (
+    "pick".equals(m.getName()) &&
+    m.isStatic() &&
+    m.isPublic()
+) {
+    pickFound = true;
+}
+else if (
+    "pick".equals(m.getName()) &&
+    m.isStatic() &&
+    m.isPublic()
+) {
+    pickFound = true;
+}
+
+String[] constraints = {                                               |
+    "patternPanel.top=form.top", "patternPanel.hcenter=form.hcenter",  |
+    "okButton.top=patternPanel.bottom+20",                             |
+    "okButton.right=form.hcenter-10", "cancelButton.vcenter=10",       |
+    "cancelButton.left=10"                                             |
+};                                                                     |
+
+String[] constraints = {                                               |
+    "patternPanel.top=form.top",                                       |
+    "patternPanel.hcenter=form.hcenter",                               |
+    "okButton.top=patternPanel.bottom+20",                             |
+    "okButton.right=form.hcenter-10",                                  |
+    "cancelButton.vcenter=10",                                         |
+    "cancelButton.left=10"                                             |
+};                                                                     |
+
+String[] constraints = {                                               |
+    "patternPanel.top=form.top", "patternPanel.hcenter=form.hcenter",
+    "okButton.top=patternPanel.bottom+20", "okButton.right=form.hcenter-10",
+    "cancelButton.vcenter=10", "cancelButton.left=10"                  |
+};                                                                     |
+
aelfred-1.2.jar
jalopy-1.0b11.jar
jalopy-ant-0.6.2.jar
jaxp-1.2.jar
jdom-1.0b8.jar
log4j-1.2.6.jar
oro-2.0.6.jar
sax-2.0.1.jar

-nodisplay	Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)
-props FILE	Use the given Jalview properties file instead + of users default.
-features FILE	+ Use the given file to add sequence features to an alignment. + See Features + File (Known as Groups file prior to 2.08) description. + +
+ -annotations FILE +	Add precalculated annotations to the alignment. See Annotation File + description.
+ -tree FILE +	+ Load the given newick format tree file onto + the alignment +
+ -questionnaire URL +	+ Queries the given URL for information about + any Jalview user questionnaires +
+ -noquestionnaire +	+ Turn off questionnaire check +
+ -nousagestats +	+ Turn off google analytics usage tracking +
+ -[no]sortbytree +	+ Enable or disable automatic sorting of associated view when a new tree is displayed +
+ -dasserver nickname=URL +	+ Add and enable a DAS server with given + nickname (alphanumeric or underscores only) for retrieval of features + for all alignments + Sources that also support the sequence command may be specified by prepending the URL with 'sequence:' + e.g. sequence:http://localdas.somewhere.org/das/source +
+ -fetchfrom nickname +	+ Query a DAS source called nickname for features for the alignments + and display them +
+ -groovy FILE +	+ Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other + arguments have been processed +
+ -vdoc VAMSAS DOCUMENT FILE or URL +	+ Import the given vamsas document into a new session. New in 2.5 +
+ -vsess VAMSAS SESSION URL +	+ Join the given vamsas session If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).New in 2.5 +
+ -groovy FILE +	+ Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other + arguments have been processed +
+ -fasta FILE +	+ Create alignment file FILE in Fasta format. +
-clustal FILE	Create alignment file FILE in Clustal format.
-msf FILE	Create alignment file FILE in MSF format.
-pileup FILE	Create alignment file FILE in Pileup format.
-pir FILE	Create alignment file FILE in PIR format.
-pfam FILE	Create alignment file FILE in PFAM format.
-blc FILE	Create alignment file FILE in BLC format.
-jalview FILE	Create alignment file FILE in Jalview format.
-png FILE	Create PNG image FILE from alignment.
-imgMap FILE	Create HTML file FILE with image map of PNG + image.
-eps FILE	Create EPS file FILE from alignment.

Type of Colouring	Icon
Graduated colour by Feature Score
Graduated colour thresholded (less than) by feature Score
Graduated colour thresholded (greater than) by feature Score
Colour by Feature Label (may also be thresholded)
+ + The current threshold is given in the + icon's tooltip.* +* +

Action	Windows	Unix	Mac/OSX
Rotate View	Left Click and Drag	Left Click and Drag	Click and Drag
Zoom	Shift + Left Click drag mouse up or down	Shift + Left Click or middle button drag + mouse up or down	Left-Alt + Click and drag mouse up or down
Select/ + Deselect + Residue	Left Click	Left Click	Click
Roll View	Shift + Left Click drag mouse to left or + right	Shift + Left Click or middle button drag mouse to left or right	Left-Alt + Click and drag mouse to left or right
Move Origin	Shift+Control+Left Click or Middle Button + + Drag	Middle-Button and drag	Shift+Control+Left Click or Middle Button + and drag
Jmol Menu	Right-Click	Right-Click	Apple-Click

Action	Windows	Unix	Mac/OSX
Select/ + Deselect + Residue	Left Click	Left Click	Click
Rotate View	Left Click and Drag	Left Click and Drag	Click and Drag
Roll View	Right Click and drag	Right Click and Drag	TODO
Move Origin	Middle-Button and Drag	Middle-Button and Drag	TODO
Zoom In	Up Arrow	Up Arrow	Up Arrow
Zoom Out	Down Arrow	Down Arrow	Down Arrow

Key	Which Mode	Action
Escape	Normal	Clears the current selection region, highlighted columns and highlghted + residues.
Escape	Cursor	As in normal mode, but also cancels any partially entered commands
F1	Both	Show Help Documentation
F2		Toggle Cursor mode on / off
Control 'Z'	Both	Undoes the last sequence edit
Control 'Y'	Both	Redo the last sequence edit undone.
Up Arrow	Normal	Moves selected sequence(s) up the alignment
Down Arrow	Normal	Moves selected sequence(s) down the alignment.
Left Arrow	Normal	Slides selected sequence(s) left. Press Alt key to slide in cursor mode
Right Arrow	Normal	Slides selected sequence(s) right. Press Alt key to slide in cursor mode
Cursor Keys + (Arrow Keys)	Cursor	Move cursor around alignment
Page Up	Both	Scroll up the alignment view
Page Down	Both	Scroll down the alignment view
Control 'A'	Both	Selects all sequences in the alignment
Control 'I'	Both	Invert sequence selection.
Control Alt 'I'	Both	Invert column selection.
Control 'C'	Both	Copies the selected region into the clipboard as a Fasta format file + nb. not available in applet, as no clipboard is available
Control 'V'	Both	Paste the contents of the clipboard to the current alignment window. + (Alignment Window->Edit->Paste->Add to this Alignment) nb. if the + paste is from a Jalview alignment, any sequence and alignment annotations + will also be copied over.
Control Shift 'V'	Both	Paste the contents of the clipboard to a new alignment window. (Alignment + Window->Edit->Paste->To New Alignment)
Control 'X'	Both	Cuts the (fully) selected sequences from the alignment. + +
Control 'F'	Both	Launches the search window
H	Both	Hides / Reveals selected columns and sequences
Control 'H'	Both	Hides / Reveals selected columns
Shift 'H'	Both	Hides / Reveals selected sequences
Control + Shift 'H'	Both	Hides everything but the current selection
Control 'O'	Both	Input new alignment from file
Control 'S'	Both	Save alignment with current filename and format
Control Shift 'S'	Both	Save alignment as a new file or with a different format
Control 'P'	Both	Opens the print dialog box to print the current view
Control 'W'	Both	Closes the current view or the current alignment
Backspace	Normal	Delete the currently selected rows or columns from the alignment.
Control 'L'	Left	Remove columns to left of left-most column marker.
Control 'R'	Both	Remove columns to right of right-most column marker.
Control 'E'	Both	Remove gapped columns
Control Shift 'E'	Both	Remove all gaps
Control 'D'	Both	Open the 'Remove redundancy' Dialog box.
	Normal

Compound +Command	Mode	Action (and parameter description)
0-9	Cursor	Begin entering a +numeric parameter (p) or repetition number for a cursor movement or edit +command.
,	Cursor	Separates one or +more numeric parameters (e.g. p1,p2) for a command.
p1,p2 Return	Cursor	Move cursor to a particular column (p1) and row (p2) in the alignment. e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.
pS	Cursor	Jump to the p'th sequence in the alignment.
pP	Cursor	Jump to p'th amino acid in current sequence.
pC	Cursor	Jump to p'th column in the alignment.
Q	Cursor	Marks the top left corner of the selection area
M	Cursor	Marks the bottom right corner of the selection area
[p] Space	Cursor	Inserts +one (or optionally p) gaps at the current position. Hold down Control or Shift to insert gaps over a sequence group
[p] Delete	Cursor	Removes +one (or optionally p) gaps at the cursor position. Hold down Control or Shift to insert gaps over a sequence group
[p] Backspace	Cursor	Removes +one (or optionally p) gaps at the cursor position. Hold down Control or Shift to insert gaps over a sequence group

Data Sharing Capability	Jalview Version
Alignments, sequences and annotation, trees, database + references, cDNA/protein mappings.	2.4
Mouseover location across linked DNA, protein and structure + positions.	2.4
Jalview project settings (Multiple views, groups, tree + partitions, colouring, window positions)	2.5
Sequence region and column selections	2.5

+Adding Groovy Support to Jalview +

Getting Groovy...

TODO

Making it easier

Building Jalview from Source

Developing Jalview

Jalview Source Documentation

Adding New Datamodel Objects To Jalview

Steps for integrating a new class into the datamodel

(Since Jalview 2.5) ROWPROPERTIES

(Since Jalview 2.2.1) SEQUENCE_GROUP

Jalview local Jnlp File

+ + Memory Usage Settings for Jalview + +

Amino Acid Properties

Acknowledgements

Bibliography

Chapter 2. Building

2.1. Prerequisites

2.2. Building

4.3.6. Comments

4.3.6.1. Remove

4.3.6.2. Format

Trackers

Mailing Lists

Contributors

Dedication

Tabacaria

Appendix A. Library Dependencies

Documentation

Downloads

Plug-ins

Sources

+Jalopy 1.0 +

4.3.8. Environment

4.3.8.1. User environment variables

4.3.8.2. System environment variables

4.3.8.3. Local environment variables

4.3.8.4. Usage

Feature list

4.3.11. Footer

4.3.10. Header

Headers and Javadoc comments

4.3.10.1. +Options +

4.3.10.1.1. General

4.3.10.1.2. Delete Headers

4.3.10.1.3. Blank lines

4.3.10.2. +Text +

1.0 Beta 10 (2002-11-14)

1.0 Beta 9 (2002-11-12)

1.0 Beta 8 (2002-08-06)

1.0 Beta 7 (2002-05-26)

1.0 Beta 6 (2002-05-19)

1.0 Beta 5 (2000-04-14)

1.0 Beta 4 (2000-03-20)

1.0 Beta 3 (2000-03-10)

1.0 Beta 2 (2002-03-05)

1.0 Beta 1 (2002-02-13)

Initial beta version (2002-02-10)

4.3.7. Imports

4.3.7.1. General

4.3.7.2. Grouping

4.3.7.3. Optimize

4.3.3. Indentation

4.3.3.1. General

4.3.3.1.1. Policy

4.3.3.1.2. Sizes

4.3.3.2. Misc

4.3.3.3. Align

4.3.3.4. Continuation

Overview

4.4.2. Naming

4.4.2.1. Regular expression tester

4.4. Code Inspector

4.4.1. General

4.4.1.1. General

4.4.1.2. Tips

Chapter 1. Installation

1.1. System requirements

Incompatibility with Sun JDK 1.4

1.2. Installing Jalopy