<classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
<classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
<classpathentry kind="lib" path="lib/VARNAv3-91.jar"/>
+
<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
<classpathentry kind="lib" path="lib/xml-apis.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin17"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
<include name="*.jar"/>
</fileset> -->
</path>
+
<!-- Jalview Version String displayed by application on startup and used to check for updates -->
<property name="JALVIEW_VERSION" value="DEVELOPMENT" />
+
+ <property name="INSTALLATION" value="Source" />
+
<!-- 2.4 (VAMSAS)" -->
<!-- Include debugging information in javac true or false -->
<property name="javac.debug" value="true" />
<properties file="${outputDir}/.build_properties">
<header>
---Jalview Build Details---
- </header>
+ </header>
<property name="VERSION" value="${JALVIEW_VERSION}" />
+ <property name="INSTALLATION" value="${INSTALLATION}" />
<property name="BUILD_DATE" value="${build.date}" />
</properties>
</target>
<mapID target="disorder" url="html/webServices/proteinDisorder.html"/>
<mapID target="aacon" url="html/webServices/AACon.html"/>
<mapID target="rnaalifold" url="html/webServices/RNAalifold.html"/>
+ <mapID target="seqannots" url="html/features/annotation.html#seqannots"/>
<mapID target="seqfetch" url="html/features/seqfetch.html"/>
<mapID target="dbreffetcher" url="html/webServices/dbreffetcher.html"/>
<mapID target="seqmappings" url="html/features/seqmappings.html"/>
<mapID target="pdbjmol" url="html/features/jmol.html"/>
<mapID target="chimera" url="html/features/chimera.html"/>
<mapID target="varna" url="html/features/varna.html"/>
+ <mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
<mapID target="preferences" url="html/features/preferences.html"/>
<mapID target="commandline" url="html/features/commandline.html"/>
<mapID target="clarguments" url="html/features/clarguments.html"/>
<tocitem text="Pairwise Alignments" target="pairwise"/>
<tocitem text="Remove Redundancy" target="redundancy"/>
</tocitem>
+ <tocitem text="Sequence Annotations" target="seqannots" expand="true">
+ <tocitem text="Annotation from Structure" target="xsspannotation" expand="false"/>
+ </tocitem>
<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
<tocitem text="Conservation" target="calcs.alconserv"/>
<tocitem text="Quality" target="calcs.alquality"/>
href="annotationsFormat.html">Annotations File</a> dragged into the
alignment window or loaded from the alignment's file menu.
</p>
+<p><a name="seqannots"/><strong>Sequence Reference Annotation</strong>
+</p>
+<p>
+ Sequence reference annotation is created from 3D structure
+ data, and from the results of sequence based prediction of
+ <a href="../webServices/jnet.html">secondary structure</a> and <a
+ href="../webServices/proteinDisorder.html">disordered region</a>
+ prediction methods.
+</p>
<p><strong>Interactive Alignment Annotation</strong></p>
<p>
Annotation rows are added using the <strong>Annotation Label</strong>
they are insertions (relative to the associated sequence in the
alignment) and grey if they are N or C terminal flanks outside the
region mapped to the alignment window's sequence.</em></li>
+ <li><strong>By Chain<br>
+ </strong><em>Uses the Chimera 'rainbow chain' command to apply a different colour to each chain.</em></li>
<li><strong>Charge & Cysteine<br>
</strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid or
Glutamic Acid) residues in red, and cationic (Lysine or Arginine)
<p><a name="structure"><strong>"Structure"
Preferences tab</strong></a><em> added in Jalview 2.8.2</em></p>
<p><em>Process secondary structure from PDB</em> - if selected, then structure information
-read from PDB will be processed to derive secondary structure annotation.
-<p><em>Use RNAView for secondary structure</em> - if selected, the RNAView service will be
-automatically called to derive secondary structure information.
-<p><em>Add secondary structure annotation to alignment</em> - if selected, PDB secondary structure
-annotation will be shown on the alignment when available.
-<p><em>Add Temperature Factor annotation to alignment</em> - if selected, PDB Temperature Factor
-annotation will be shown on the alignment when available.
+read from PDB will be processed and annotation added to associated sequences.
+<p><em>Use RNAView for secondary structure</em> - if selected, the pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>) will be
+called to derive secondary structure information for RNA chains.
+<p><em>Add secondary structure annotation to alignment</em> - if selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's implementation DSSP</a> will be used to add annotation to polypeptide chains in the structure.
+<p><em>Add Temperature Factor annotation to alignment</em> - if selected, values extracted from the Temperature Factor
+column for the backbone atoms in the PDB file will be extracted as annotation lines shown on the alignment.
<p><em>Default structure viewer</em> - choose JMOL or CHIMERA for viewing 3D structures.
<p><em>Path to Chimera program</em> - Optional, as Jalview will search standard installation paths for Windows, Linux or MacOS.
-If you have installed Chimera in a non-standard location, you can specify it here. Enter the full path to the Chimera executable program.
+If you have installed Chimera in a non-standard location, you can specify it here, by entering the full path to the Chimera executable program.
+Double-click this field to open a file chooser dialog.
<p><a name="connections"><strong>"Connections"
Preferences tab</strong></a></p>
</head>
<body>
<p><strong>Viewing PDB Structures</strong></p>
-
-<p>Jalview can view protein structures associated with a sequence
-via the <strong>"Structure→"</strong> submenu from a
-sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.</p>
-A <a href="jmol.html">Jmol viewer</a> has been included since Jalview 2.3. Jalview 2.8.2 added support for <a href="https://www.cgl.ucsf.edu/chimera/">Chimera</a>,
-provided this has been separately installed. Choice of default viewer is configurable in the Preferences <a href="preferences.html#structure">Structure tab</a>.
-
-<p>The following menu entries are provided for viewing structure data<br>
+ <p>
+ Jalview can view protein structures associated with a sequence via the
+ <strong>"Structure→"</strong> submenu from a sequence's <a
+ href="../menus/popupMenu.html">pop-up menu</a>.
+ </p>
+ The
+ <a href="jmol.html">Jmol viewer</a> has been included since Jalview
+ 2.3. Jalview 2.8.2 included support for
+ <a href="https://www.cgl.ucsf.edu/chimera/">Chimera</a>, provided it is
+ installed and can be launched by Jalview. The default viewer can be
+ configured in the
+ <a href="preferences.html#structure">Structure tab</a> in the
+ <strong>Tools→Preferences</strong> dialog box.
+ <p>
+ Structure data imported into Jalview can also be processed to display
+ secondary structure and temperature factor annotation. See the <a
+ href="xsspannotation.html">Annotation from Structure</a> page for
+ more information.
+ </p>
+ <p>The following menu entries are provided for viewing structure data<br>
<ul>
<li>The <strong>"Structure→View
Structure→</strong> submenu allows a single PDB structure to be chosen
--- /dev/null
+<html>
+<!--
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Annotation from 3D structure data</title>
+</head>
+<body>
+ <p>
+ <strong>Working with annotation from 3D structure data</strong>
+ </p>
+ <p>
+ Jalview can process PDB data associated with sequences to display
+ values extracted from the <em>Temperature Factor</em> column for
+ corresponding sites, and secondary structure from DSSP or RNAView (as
+ appropriate).
+ </p>
+ <p>
+ <strong>Extracting data from PDB files<br /></strong>Annotation is
+ created for structure files retrieved directly from the PDB loaded
+ from the file system (via the <strong>Structure→Associate
+ Structure...→From file</strong> option, or when displayed via the View
+ Structures Menu.<br /> Structure annotation is not automatically
+ added to an alignment, but any available structure annotation rows for
+ the current selection or a particular sequence can be added via the <strong>Add
+ Reference Annotation</strong> in the <strong>Selection</strong> and <strong>Sequence
+ ID</strong> sub-menus of the Sequence ID Panel's popup menu.<br/> <em>Please
+ note:</em>Protein structures are analysed
+ <em>in situ</em>, but Jalview employs a web service to process RNA
+ structures which can cause long delays if your internet connection is
+ slow.
+ </p>
+ <p>
+ The <a href="../menus/alwannotation.html"><em>Annotations</em>
+ alignment menu</a> provides settings useful for controlling the display
+ of secondary structure annotation.
+ </p>
+ <p>
+ <strong>Shading sequences by associated structure annotation<br /></strong>The
+ annotation colouring dialog (opened by the <strong>Colour→By
+ Annotation</strong> option) allows sequences with associated secondary
+ structure data to be shaded according to secondary structure type.
+ Once the dialog is opened, select the <em>Per Sequence</em> option and
+ then choose <em>Secondary structure</em> from the dropdown menu.<br />When
+ colouring alignments by secondary structure, two modes can be
+ employed. The default is to shade sequences with the same colour as
+ the secondary structure glyph. If, however, <em>original colours</em>
+ is selected and another colourscheme has already been applied, then
+ only portions of the sequence with defined secondary structure will be
+ shaded with the previously applied scheme.<br />
+ </p>
+ <p>
+ <strong>Configuration options for processing PDB files<br /></strong>
+ Occasionally, you may wish to disable secondary structure processing.
+ Configuration options in the <strong>Structure</strong> tab in the <strong>Tools→Preferences</strong>
+ dialog allow the processing of structure data to be disabled, or
+ selectively enabled. For more information, take a look at the <a href="preferences.html#structure">documentation for the structure panel</a>.
+ </p>
+ <p>
+ <em>The display of secondary structure data was introduced in
+ Jalview 2.8.2, and is made possible by Jalview's use of <a
+ href="jmol.html">Jmol's DSSP implementation</a>, based on the
+ original <a href="http://www.ncbi.nlm.nih.gov/pubmed/6667333">Kabsch
+ and Sander algorithm</a> ported by <a
+ href="http://swift.cmbi.ru.nl/gv/dssp/">Robbie P. Joosten and
+ colleagues</a>, and a client for <a
+ href="https://github.com/fjossinet/PyRNA">Fabrice Jossinet's
+ pyRNA services</a> that was developed by Anne Menard, Jim Procter and
+ Yann Ponty as part of the Jalview Summer of Code 2012.
+ </em>
+ </p>
+</body>
+</html>
<li><strong>Hide Annotations...<br>
</strong><em>Choose to hide either All or
a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
- <li><strong>Add Reference Annotations...<br>
+ <li><a name="addrefannot"><strong>Add Reference Annotations<br>
</strong><em>Add to the alignment window any annotations on the selected sequences
which have been read from reference sources or calculated (for example,
secondary structure derived from 3D structure). (Since Jalview 2.8.2)</em></li>
window will be displayed asking for a new sequence name and sequence description
to be entered. Press OK to accept your edit. To save sequence descriptions,
you must save in Fasta, PIR or Jalview File format.</em></li>
- <li><em> </em></li>
+ <li><a href="sqaddrefannot"><strong>Add Reference Annotations<br></strong><em>When enabled, copies any available alignment annotation for this sequence to the current view.</em></li>
<li><strong>Represent Group With (Sequence Id)</strong><br>
<em>All sequences in the current selection group will be hidden, apart
from (Sequence Id). Any edits performed on the visible representative
</tr>
<tr>
<td><div align="center">
+ <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>18/11/2014</em></strong>
+ </div></td>
+ <td>
+ <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
+ <em>General</em>
+ <ul>
+ </ul> <em>Application</em>
+ <ul>
+ <li>Update Jalview project format:
+ <ul>
+ </ul>
+ </li>
+ </ul>
+ </td>
+ <td>
+ <!-- issues resolved --> <em>Application</em>
+ <ul>
+
+ </ul> <em>Applet</em>
+ <ul>
+ </ul> <em>Other</em>
+ <ul>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td><div align="center">
<strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
</div></td>
<td>
invoked to rationalise significantly different primary predictions.</em></li>
</ul>
</p>
+<em>JNet annotation created in Jalview 2.8.2 and later versions can be displayed on other alignments via the <a href="">Add reference annotation</a></em>
<em>As of Jalview 2.6, the Jnet service accessed accessed via the
'Secondary structure prediction' submenu should be considered a legacy
Jalview SOAP service, and will be replaced in the near future by a
-JABAWS Jnet service.</em>
+JABAWS Jnet service (now available in the Jalview 2.9 development version).</em>
</body>
</html>
</head>
<body>
<p>
- <strong>What's new ?</strong></p>
- <p>
- Jalview 2.8.1 includes new features for group creation, RNA secondary
- structure prediction and a host bug fixes. It also includes support
- for <a href="http://www.compbio.dundee.ac.uk/JABAWS">version 2.1
- of JABA</a> and includes a Spanish translation of its user interface.<br />
- The highlights are detailed below, and the full list is given in the <a
- href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
- </p>
- <p>The Desktop and web based applet include new keystrokes for
- defining and undefining groups, and PAM250 has been added to the range
- of score models available for use by the tree and PCA calculations.
- The Jalview project file format has also been extended for handling
- RNA and protein secondary structure annotation, in anticipation for
- new structure based secondary structure support in Jalview 2.8.2.</p>
- <p><strong>Internationalisation</strong></p>
- <p>Jalview 2.8.1 is the first release to include support for
- displaying Jalview's user interface in different languages. In August
- 2013, David Roldán-Martinez took on the task of
- internationalising Jalview's user interface. He also recruited Sara
- Hernández Díaz and Laura Ferrandis Martinez who created
- Jalview's first spanish user interface translation.</p>
- <p>
- If you notice any problems, or would like to help translate Jalview's
- user interface into other languages, head over to <a
- href="http://issues.jalview.org">issues.jalview.org</a> and put in a
- feature request describing the translations you can provide to the <a
- href="http://issues.jalview.org/browse/JAL/component/10682">i18n
- component</a>. David has also <a
- href="https://wiki.jalview.org/index.php/Development:i18n">documented
- the process of creating i18n translations</a> to help you get started.
+ <strong>What's new ?</strong>
</p>
- <p><strong>RNA Secondary Structure Prediction with JABA 2.1</strong></p>
- <p>
- This version of Jalview includes a client to access the new services available in <a
- href="http://www.compbio.dundee.ac.uk/jabaws/">JABA v2.1</a> , which
- provides services for RNA consensus secondary structure prediction and
- two new alignment programs (<a
- href="http://sourceforge.net/projects/glprobs/">GLProbs</a> and <a
- href="http://sourceforge.net/projects/msaprobs/">MSAProbs</a>).</p>
<p>
- To see how to perform RNA secondary structure predictions like the one below, take a look at the <a href="webServices/RNAalifold.html">RNAAliFold
- client documentation</a>.
+ Jalview 2.8.2 is the first release produced by our new core
+ development team.<br /> It incorporates many minor improvements and
+ bug-fixes, and also includes new features for working with 3D
+ structure data, shading alignments by secondary structure and
+ generation of alignment figures as Scalable Vector Graphics. <br />As
+ ever, the highlights are detailed below, and the full list is given in
+ the <a href="releases.html#Jalview2.8.2">Jalview 2.8.2 Release
+ Notes</a>.
</p>
- <div align="center">
- <img src="webServices/RNAalifoldAnnotationRows.png" width="500" height="216"> <br> <em>The RNAalifold client was implemented by Jalview's 2013
- summer student, Dan Barton.</em>
- </div>
</body>
</html>
action.apply = Apply
action.apply_threshold_all_groups = Apply threshold to all groups
action.apply_all_groups = Apply to all Groups
-action.by_chain = By chain
+action.by_chain = By Chain
action.by_sequence = By Sequence
action.paste_annotations = Paste Annotations
action.format = Format
label.autoadd_temp = Add Temperature Factor annotation to alignment
label.structure_viewer = Default structure viewer
label.chimera_path = Path to Chimera program
-label.chimera_path_tip = Jalview will try standard locations, plus any path entered here.
-label.invalid_path = File not found or not executable
+label.chimera_path_tip = Jalview will first try any path entered here, else standard installation locations.<br>Double-click to browse for file.
+label.invalid_chimera_path = Chimera path not found or not executable
label.min_colour = Minimum Colour
label.max_colour = Maximum Colour
label.use_original_colours = Use Original Colours
label.select_eps_character_rendering_style = Select EPS character rendering style
label.invert_selection = Invert Selection
label.optimise_order = Optimise Order
-label.seq_sort_by_score = Seq sort by Score
+label.seq_sort_by_score = Sequence sort by Score
label.load_colours = Load Colours
label.save_colours = Save Colours
label.fetch_das_features = Fetch DAS Features
label.rest_client_submit = {0} using {1}
label.fetch_retrieve_from =Retrieve from {0}</html>
label.fetch_retrieve_from_all_sources = Retrieve from all {0} sources in {1}<br>First is :{2}<html>
-label.feature_settings_click_drag = <html>Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/></html>
+#label.feature_settings_click_drag = <html>Click/drag feature types up or down to change render order.<br/>Double click to select columns containing feature in alignment/current selection<br/>Pressing Alt will select columns outside features rather than inside<br/>Pressing Shift to modify current selection (rather than clear current selection)<br/>Press CTRL or Command/Meta to toggle columns in/outside features<br/></html>
+label.feature_settings_click_drag = Drag up or down to change render order.<br/>Double click to select columns containing feature.
+label.transparency_tip = Adjust transparency to 'see through' feature colours.
label.opt_and_params_further_details = see further details by right-clicking
label.opt_and_params_show_brief_desc_image_link = <html>Click to show brief description<br><img src="{0}"/> Right click for further information.</html>
label.opt_and_params_show_brief_desc = <html>Click to show brief description<br></html>
label.rest_client_submit = {0} utilizando {1}
label.fetch_retrieve_from =Recuperar de {0}
label.fetch_retrieve_from_all_sources = Recuperar de todas las fuentes {0} en {1}<br>La primera es :{2}
-label.feature_settings_click_drag = Haga clic o arrastre los tipos de las caracterÃsticas hacia arriba o hacia abajo para cambiar el orden de visualización.<br/>Haga doble clic para seleccionar las columnas que contienen las caracterÃsticas del alineamiento/selección actual.<br/>Presionando Alt seleccionará las columnas exteriores a las caracterÃsticas en lugar de las interiores<br/>Presione Shift para modificar la selección actual (en lugar de borrarla)<br/>Presione CTRL o Command/Meta para cambiar las columans externas o internas a las caracterÃsticas<br/>
+label.feature_settings_click_drag = Haga clic o arrastre los tipos de las caracterÃsticas hacia arriba o hacia abajo para cambiar el orden de visualización.<br/>Haga doble clic para seleccionar las columnas que contienen las caracterÃsticas del alineamiento/selección actual.<br/>
label.opt_and_params_further_details = ver los detalles adicionales haciendo clic en el botón derecho
label.opt_and_params_show_brief_desc_image_link = Haga clic para ver una descripción breve<br><img src="{0}"/>Haga clic en el botón derecho para obtener información adicional.
label.opt_and_params_show_brief_desc = Haga clic para ver una descripción breve<br>
bonds.addElement(new Bond(start, end, at1, at2));
}
- public void makeResidueList()
+ public void makeResidueList(boolean visibleChainAnnotation)
{
int count = 0;
Object symbol;
.elementAt(i));
resFeatures.setElementAt(null, i);
}
- Annotation[] annots = new Annotation[resAnnotation.size()];
- float max = 0;
- for (i = 0, iSize = annots.length; i < iSize; i++)
+ if (visibleChainAnnotation)
{
- annots[i] = (Annotation) resAnnotation.elementAt(i);
- if (annots[i].value > max)
+ Annotation[] annots = new Annotation[resAnnotation.size()];
+ float max = 0;
+ for (i = 0, iSize = annots.length; i < iSize; i++)
{
- max = annots[i].value;
+ annots[i] = (Annotation) resAnnotation.elementAt(i);
+ if (annots[i].value > max)
+ {
+ max = annots[i].value;
+ }
+ resAnnotation.setElementAt(null, i);
}
- resAnnotation.setElementAt(null, i);
+
+ AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+ "Temperature Factor", "Temperature Factor for " + pdbid + id,
+ annots, 0, max,
+ AlignmentAnnotation.LINE_GRAPH);
+ tfactorann.setSequenceRef(sequence);
+ sequence.addAlignmentAnnotation(tfactorann);
}
- AlignmentAnnotation tfactorann = new AlignmentAnnotation(
- "PDB.TempFactor", "Temperature Factor for "
- + sequence.getName(), annots, 0, max,
- AlignmentAnnotation.LINE_GRAPH);
- tfactorann.setSequenceRef(sequence);
- sequence.addAlignmentAnnotation(tfactorann);
}
public void setChargeColours()
}
}
}
- float min = -1, max = 0;
- Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
- for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
+ if (false)
{
- int prn = mapping.getPDBResNum(k + 1);
-
- an[k] = new Annotation(prn);
- if (min == -1)
- {
- min = k;
- max = k;
- }
- else
+ // Useful for debugging mappings - adds annotation for mapped position
+ float min = -1, max = 0;
+ Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
+ for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
{
- if (min > k)
+ int prn = mapping.getPDBResNum(k + 1);
+
+ an[k] = new Annotation(prn);
+ if (min == -1)
{
min = k;
+ max = k;
}
- else if (max < k)
+ else
{
- max = k;
+ if (min > k)
+ {
+ min = k;
+ }
+ else if (max < k)
+ {
+ max = k;
+ }
}
}
+ sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+ "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+ an, min, max, AlignmentAnnotation.LINE_GRAPH));
}
- sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
- "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
- an, min, max, AlignmentAnnotation.LINE_GRAPH));
-
}
}
}
try
{
tmpPDBFile = pdbentry.getFile();
- PDBfile pdbfile = new PDBfile(false,false,tmpPDBFile,
+ PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
jalview.io.AppletFormatAdapter.FILE);
pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
*/
boolean VisibleChainAnnotation = false;
- boolean processSecondaryStructure=true;
-
+ boolean processSecondaryStructure = true;
+
+ boolean externalSecondaryStructure = false;
public PDBfile(boolean visibleChainAnnotation,
- boolean processSecondaryStructure)
+ boolean processSecondaryStructure, boolean externalSecStr)
{
super();
VisibleChainAnnotation = visibleChainAnnotation;
this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
}
public PDBfile(boolean visibleChainAnnotation,
- boolean processSecondaryStructure, String file, String protocol) throws IOException
+ boolean processSecondaryStructure, boolean externalSecStr,
+ String file, String protocol) throws IOException
{
super(false, file, protocol);
VisibleChainAnnotation = visibleChainAnnotation;
this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
doParse();
}
public PDBfile(boolean visibleChainAnnotation,
- boolean processSecondaryStructure, FileParse source) throws IOException
+ boolean processSecondaryStructure, boolean externalSecStr,
+ FileParse source) throws IOException
{
super(false, source);
VisibleChainAnnotation = visibleChainAnnotation;
this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
doParse();
}
entry.setProperty(new Hashtable());
if (chains.elementAt(i).id != null)
{
- entry.getProperty().put("CHAIN",
- chains.elementAt(i).id);
+ entry.getProperty().put("CHAIN", chains.elementAt(i).id);
}
if (inFile != null)
{
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
- if (chainannot != null)
+ if (chainannot != null && VisibleChainAnnotation)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
}
if (processSecondaryStructure)
{
- if (rna.size() > 0)
- {
- try
+ if (externalSecondaryStructure && rna.size() > 0)
{
- processPdbFileWithAnnotate3d(rna);
- } catch (Exception x)
- {
- System.err
- .println("Exceptions when dealing with RNA in pdb file");
- x.printStackTrace();
+ try
+ {
+ processPdbFileWithAnnotate3d(rna);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+ }
}
- }
- ;
- if (prot.size() > 0)
- {
- try
+ ;
+ if (prot.size() > 0)
{
- processPdbFileWithJmol(prot);
- } catch (Exception x)
- {
- System.err
- .println("Exceptions from Jmol when processing data in pdb file");
- x.printStackTrace();
+ try
+ {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions from Jmol when processing data in pdb file");
+ x.printStackTrace();
+ }
}
}
- }
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
public static boolean isCalcIdHandled(String calcId)
{
- return calcId != null
- && (calcIdPrefix.equals(calcId));
+ return calcId != null && (calcIdPrefix.equals(calcId));
}
- public static boolean isCalcIdForFile(AlignmentAnnotation alan, String pdbFile)
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+ String pdbFile)
{
return alan.getCalcId() != null
&& calcIdPrefix.equals(alan.getCalcId())
{
for (SequenceI sq : seqs)
{
- for (AlignmentAnnotation aa : sq.getAnnotation())
+ if (sq.getAnnotation() != null)
{
- String oldId = aa.getCalcId();
- if (oldId == null)
+ for (AlignmentAnnotation aa : sq.getAnnotation())
{
- oldId = "";
+ String oldId = aa.getCalcId();
+ if (oldId == null)
+ {
+ oldId = "";
+ }
+ aa.setCalcId(calcIdPrefix);
+ aa.setProperty("PDBID", id);
+ aa.setProperty("oldCalcId", oldId);
}
- aa.setCalcId(calcIdPrefix);
- aa.setProperty("PDBID", id);
- aa.setProperty("oldCalcId", oldId);
}
}
}
+
private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
throws Exception
{
AlignmentI al, String pep, boolean b)
{
List<List<? extends Object>> replaced = AlignSeq
- .replaceMatchingSeqsWith(seqs,
- annotations, prot, al, AlignSeq.PEP, false);
+ .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
+ false);
for (PDBChain ch : chains)
{
int p = 0;
p = -p - 1;
// set shadow entry for chains
ch.shadow = (SequenceI) replaced.get(1).get(p);
- ch.shadowMap = ((AlignSeq) replaced.get(2)
-.get(p))
+ ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
.getMappingFromS1(false);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- chains.elementAt(i).makeResidueList();
+ chains.elementAt(i).makeResidueList(VisibleChainAnnotation);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- chains.elementAt(i).setChainColours(Color.getHSBColor(
- 1.0f / i, .4f, 1.0f));
+ chains.elementAt(i).setChainColours(
+ Color.getHSBColor(1.0f / i, .4f, 1.0f));
}
}
ap++;
}
}
- if (sq.getAnnotation() != null)
+ if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
{
annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
}
public void sort(AlignmentAnnotation[] alignmentAnnotations,
SequenceAnnotationOrder order)
{
+ if (alignmentAnnotations == null)
+ {
+ return;
+ }
// cache 'alignment sequence position' for the annotations
saveSequenceIndices(alignmentAnnotations);
package jalview.analysis;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.datamodel.SequenceFeature;
+import jalview.util.MessageManager;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Stack;
import java.util.Vector;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.datamodel.SequenceFeature;
-import jalview.util.MessageManager;
-
public class Rna
{
{
for (int i = 0; i < openingPars.length; i++)
{
- System.out.println(closingPars[i] + "->" + openingPars[i]);
+ // System.out.println(closingPars[i] + "->" + openingPars[i]);
put(closingPars[i], openingPars[i]);
}
}
public static Vector<SimpleBP> GetSimpleBPs(CharSequence line)
throws WUSSParseException
{
- System.out.println(line);
Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
Vector<SimpleBP> pairs = new Vector<SimpleBP>();
int i = 0;
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.MessageManager;
-import jalview.util.UrlLink;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.commands.ChangeCaseCommand;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.UrlLink;
+
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Vector;
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
if (sg != null)
{
if (seq == null)
+ {
seq = (Sequence) sg.getSequenceAt(0);
+ }
EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
sg.getStartRes(), sg.getEndRes() + 1), null,
if (dialog.accept)
{
EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
- EditCommand.REPLACE, dialog.getName().replace(' ',
+ Action.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1,
PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
if (ap.av.applet.jmolAvailable)
+ {
new jalview.appletgui.AppletJmol(entry, new Sequence[]
{ seq }, null, ap, AppletFormatAdapter.URL);
+ }
else
+ {
new MCview.AppletPDBViewer(entry, new Sequence[]
{ seq }, null, ap, AppletFormatAdapter.URL);
+ }
}
else
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
}
// !newAlignment
- addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"), Action.PASTE,
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
viewport.setSelectionGroup(null);
anot[index] = new Annotation(label, "", type, 0);
}
- anot[index].secondaryStructure = type;
+
+ anot[index].secondaryStructure = type != 'S' ? type : label
+ .length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
}
}
*/
package jalview.appletgui;
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-import java.awt.event.*;
-
import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
public class RedundancyPanel extends SliderPanel implements Runnable,
WindowListener
{
}
EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
- EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
+ Action.CUT, deleted, 0, width, ap.av.getAlignment());
AlignmentI alignment = ap.av.getAlignment();
for (int i = 0; i < del.size(); i++)
{
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
import jalview.structure.SelectionSource;
import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
+
public class SeqPanel extends Panel implements MouseMotionListener,
MouseListener, SequenceListener
{
void setCursorPosition()
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ SequenceI sequence = av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ SequenceI sequence = av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
String tmp = sequence.hashCode() + index + "";
if (lastMessage == null || !lastMessage.equals(tmp))
+ {
ssm.mouseOverSequence(sequence, index, pos, av);
+ }
lastMessage = tmp;
}
int respos = sequence.findPosition(res);
if (ssm != null)
+ {
mouseOverSequence(sequence, res, respos);
+ }
StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
+ sequence.getName());
.containsKey(features[i].featureGroup)
&& !((Boolean) seqCanvas.fr.featureGroups
.get(features[i].featureGroup)).booleanValue())
+ {
continue;
+ }
if ((features[i].getBegin() <= res)
&& (features[i].getEnd() >= res))
{
if (av.isHiddenRepSequence(seq))
{
- sg = (SequenceGroup) av.getRepresentedSequences(seq);
+ sg = av.getRepresentedSequences(seq);
groupEditing = true;
}
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
startres, startres - lastres, av.getAlignment(), true);
}
}
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
startres, lastres - startres, av.getAlignment(), true);
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+ editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
{ seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
if (max > 0)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+ editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
{ seq }, startres, max, av.getAlignment(), true);
}
}
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+ editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
av.getAlignment(), true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
+ editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
av.getAlignment(), true);
}
return;
}
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if (sequence == null || res > sequence.getLength())
{
* <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
* </li>
+ * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
* <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
* warning dialog box is displayed.</li>
* <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
import jalview.gui.Desktop;
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.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;
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")
}
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)
{
}
}
+ 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"
+ + "-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)
{
/**
public static boolean debug = false;
- static String builddate = null, version = null;
+ static String builddate = null, version = null, installation = null;
private static void initBuildDetails()
{
{
builddate = "unknown";
version = "test";
+ installation = "Webstart";
java.net.URL url = JalviewLite.class
.getResource("/.build_properties");
if (url != null)
{
builddate = line.substring(line.indexOf("=") + 1);
}
+ if (line.indexOf("INSTALLATION") > -1)
+ {
+ installation = line.substring(line.indexOf("=") + 1);
+ }
}
} catch (Exception ex)
{
return builddate;
}
+ public static String getInstallation()
+ {
+ initBuildDetails();
+ return installation;
+ }
+
public static String getVersion()
{
initBuildDetails();
System.err.println("JalviewLite Version " + getVersion());
System.err.println("Build Date : " + getBuildDate());
+ System.err.println("Installation : " + getInstallation());
}
String externalsviewer = getParameter("externalstructureviewer");
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.ListIterator;
/**
*
*/
public class EditCommand implements CommandI
{
- public static final int INSERT_GAP = 0;
-
- public static final int DELETE_GAP = 1;
-
- public static final int CUT = 2;
-
- public static final int PASTE = 3;
-
- public static final int REPLACE = 4;
-
- public static final int INSERT_NUC = 5;
+ public enum Action
+ {
+ INSERT_GAP, DELETE_GAP, CUT, PASTE, REPLACE, INSERT_NUC
+ };
- Edit[] edits;
+ private List<Edit> edits = new ArrayList<Edit>();
String description;
this.description = description;
}
- public EditCommand(String description, int command, SequenceI[] seqs,
+ public EditCommand(String description, Action command, SequenceI[] seqs,
int position, int number, AlignmentI al)
{
this.description = description;
- if (command == CUT || command == PASTE)
+ if (command == Action.CUT || command == Action.PASTE)
{
- edits = new Edit[]
- { new Edit(command, seqs, position, number, al) };
+ setEdit(new Edit(command, seqs, position, number, al));
}
performEdit(0, null);
}
- public EditCommand(String description, int command, String replace,
+ public EditCommand(String description, Action command, String replace,
SequenceI[] seqs, int position, int number, AlignmentI al)
{
this.description = description;
- if (command == REPLACE)
+ if (command == Action.REPLACE)
{
- edits = new Edit[]
- { new Edit(command, seqs, position, number, al, replace) };
+ setEdit(new Edit(command, seqs, position, number, al, replace));
}
performEdit(0, null);
}
+ /**
+ * Set the list of edits to the specified item (only).
+ *
+ * @param e
+ */
+ protected void setEdit(Edit e)
+ {
+ edits.clear();
+ edits.add(e);
+ }
+
+ /**
+ * Add the given edit command to the stored list of commands.
+ *
+ * @param e
+ */
+ protected void addEdit(Edit e)
+ {
+ edits.add(e);
+ }
+
+ /**
+ * Clear the list of stored edit commands.
+ *
+ */
+ protected void clearEdits()
+ {
+ edits.clear();
+ }
+
+ /**
+ * Returns the i'th stored Edit command.
+ *
+ * @param i
+ * @return
+ */
+ protected Edit getEdit(int i)
+ {
+ if (i >= 0 && i < edits.size())
+ {
+ return edits.get(i);
+ }
+ return null;
+ }
+
@Override
final public String getDescription()
{
@Override
public int getSize()
{
- return edits == null ? 0 : edits.length;
+ return edits.size();
}
+ /**
+ * Return the alignment for the first edit (or null if no edit).
+ *
+ * @return
+ */
final public AlignmentI getAlignment()
{
- return edits[0].al;
+ return (edits.isEmpty() ? null : edits.get(0).al);
}
/**
* @param al
* @param performEdit
*/
- final public void appendEdit(int command, SequenceI[] seqs, int position,
+ final public void appendEdit(Action command, SequenceI[] seqs,
+ int position,
int number, AlignmentI al, boolean performEdit)
{
appendEdit(command, seqs, position, number, al, performEdit, null);
* @param performEdit
* @param views
*/
- final public void appendEdit(int command, SequenceI[] seqs, int position,
+ final public void appendEdit(Action command, SequenceI[] seqs,
+ int position,
int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
{
Edit edit = new Edit(command, seqs, position, number,
edit.fullAlignmentHeight = true;
}
- if (edits != null)
- {
- Edit[] temp = new Edit[edits.length + 1];
- System.arraycopy(edits, 0, temp, 0, edits.length);
- edits = temp;
- edits[edits.length - 1] = edit;
- }
- else
- {
- edits = new Edit[]
- { edit };
- }
+ edits.add(edit);
if (performEdit)
{
- performEdit(edits.length - 1, views);
+ performEdit(edit, views);
}
}
+ /**
+ * Execute all the edit commands, starting at the given commandIndex
+ *
+ * @param commandIndex
+ * @param views
+ */
final void performEdit(int commandIndex, AlignmentI[] views)
{
- int eSize = edits.length;
- for (int e = commandIndex; e < eSize; e++)
+ ListIterator<Edit> iterator = edits.listIterator(commandIndex);
+ while (iterator.hasNext())
{
- switch (edits[e].command)
- {
- case INSERT_GAP:
- insertGap(edits[e]);
- break;
- case DELETE_GAP:
- deleteGap(edits[e]);
- break;
- case CUT:
- cut(edits[e], views);
- break;
- case PASTE:
- paste(edits[e], views);
- break;
- case REPLACE:
- replace(edits[e]);
- break;
+ Edit edit = iterator.next();
+ performEdit(edit, views);
+ }
+ }
+
+ /**
+ * Execute one edit command in all the specified alignment views
+ *
+ * @param edit
+ * @param views
+ */
+ protected void performEdit(Edit edit, AlignmentI[] views)
+ {
+ switch (edit.command)
+ {
+ case INSERT_GAP:
+ insertGap(edit);
+ break;
+ case DELETE_GAP:
+ deleteGap(edit);
+ break;
+ case CUT:
+ cut(edit, views);
+ break;
+ case PASTE:
+ paste(edit, views);
+ break;
+ case REPLACE:
+ replace(edit);
+ break;
+ case INSERT_NUC:
// TODO:add deleteNuc for UNDO
// case INSERT_NUC:
// insertNuc(edits[e]);
- // break;
- }
+ break;
+ default:
+ break;
}
}
performEdit(0, views);
}
+ /**
+ * Undo the stored list of commands, in reverse order.
+ */
@Override
final public void undoCommand(AlignmentI[] views)
{
- for(Edit e : edits){
- switch (e.command)
- {
- case INSERT_GAP:
- deleteGap(e);
- break;
- case DELETE_GAP:
- insertGap(e);
- break;
- case CUT:
- paste(e, views);
- break;
- case PASTE:
- cut(e, views);
- break;
- case REPLACE:
- replace(e);
- break;
- }
+ ListIterator<Edit> iterator = edits.listIterator(edits.size());
+ while (iterator.hasPrevious())
+ {
+ Edit e = iterator.previous();
+ switch (e.command)
+ {
+ case INSERT_GAP:
+ deleteGap(e);
+ break;
+ case DELETE_GAP:
+ insertGap(e);
+ break;
+ case CUT:
+ paste(e, views);
+ break;
+ case PASTE:
+ cut(e, views);
+ break;
+ case REPLACE:
+ replace(e);
+ break;
+ case INSERT_NUC:
+ // not implemented
+ break;
+ default:
+ break;
+ }
}
}
- final void insertGap(Edit command)
+ /**
+ * Insert gap(s) in sequences as specified by the command, and adjust
+ * annotations.
+ *
+ * @param command
+ */
+ final private void insertGap(Edit command)
{
for (int s = 0; s < command.seqs.length; s++)
// adjustAnnotations(command, true, false, null);
// }
- final void deleteGap(Edit command)
+ /**
+ * Delete gap(s) in sequences as specified by the command, and adjust
+ * annotations.
+ *
+ * @param command
+ */
+ final private void deleteGap(Edit command)
{
for (int s = 0; s < command.seqs.length; s++)
{
adjustAnnotations(command, false, false, null);
}
+ /**
+ * Carry out a Cut action. The cut characters are saved in case Undo is
+ * requested.
+ *
+ * @param command
+ * @param views
+ */
void cut(Edit command, AlignmentI[] views)
{
boolean seqDeleted = false;
for (int i = 0; i < command.seqs.length; i++)
{
- if (command.seqs[i].getLength() > command.position)
+ final SequenceI sequence = command.seqs[i];
+ if (sequence.getLength() > command.position)
{
- command.string[i] = command.seqs[i].getSequence(command.position,
+ command.string[i] = sequence.getSequence(command.position,
command.position + command.number);
- SequenceI oldds = command.seqs[i].getDatasetSequence();
+ SequenceI oldds = sequence.getDatasetSequence();
if (command.oldds != null && command.oldds[i] != null)
{
// we are redoing an undone cut.
- command.seqs[i].setDatasetSequence(null);
+ sequence.setDatasetSequence(null);
}
- command.seqs[i].deleteChars(command.position, command.position
+ sequence.deleteChars(command.position, command.position
+ command.number);
if (command.oldds != null && command.oldds[i] != null)
{
// oldds entry contains the cut dataset sequence.
- command.seqs[i].setDatasetSequence(command.oldds[i]);
+ sequence.setDatasetSequence(command.oldds[i]);
command.oldds[i] = oldds;
}
else
{
// modify the oldds if necessary
- if (oldds != command.seqs[i].getDatasetSequence()
- || command.seqs[i].getSequenceFeatures() != null)
+ if (oldds != sequence.getDatasetSequence()
+ || sequence.getSequenceFeatures() != null)
{
if (command.oldds == null)
{
adjustFeatures(
command,
i,
- command.seqs[i].findPosition(command.position),
- command.seqs[i].findPosition(command.position
+ sequence.findPosition(command.position),
+ sequence.findPosition(command.position
+ command.number), false);
}
}
}
- if (command.seqs[i].getLength() < 1)
+ if (sequence.getLength() < 1)
{
- command.al.deleteSequence(command.seqs[i]);
+ command.al.deleteSequence(sequence);
seqDeleted = true;
}
}
adjustAnnotations(command, false, seqDeleted, views);
}
+ /**
+ * Perform the given Paste command. This may be to add cut or copied sequences
+ * to an alignment, or to undo a 'Cut' action on a region of the alignment.
+ *
+ * @param command
+ * @param views
+ */
void paste(Edit command, AlignmentI[] views)
{
StringBuffer tmp;
if (modifyVisibility && !insert)
{
// only occurs if a sequence was added or deleted.
- command.deletedAnnotationRows = new Hashtable();
+ command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
}
if (command.fullAlignmentHeight)
{
&& command.deletedAnnotationRows
.containsKey(command.seqs[s]))
{
- AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows
+ AlignmentAnnotation[] revealed = command.deletedAnnotationRows
.get(command.seqs[s]);
command.seqs[s].setAlignmentAnnotation(revealed);
if (revealed != null)
if (!insert)
{
- command.deletedAnnotations = new Hashtable();
+ command.deletedAnnotations = new Hashtable<String, Annotation[]>();
}
int aSize;
&& command.deletedAnnotations
.containsKey(annotations[a].annotationId))
{
- Annotation[] restore = (Annotation[]) command.deletedAnnotations
+ Annotation[] restore = command.deletedAnnotations
.get(annotations[a].annotationId);
System.arraycopy(restore, 0, temp, command.position,
&& command.deletedAnnotations
.containsKey(annotations[a].annotationId))
{
- Annotation[] restore = (Annotation[]) command.deletedAnnotations
+ Annotation[] restore = command.deletedAnnotations
.get(annotations[a].annotationId);
temp = new Annotation[annotations[a].annotations.length
if (command.editedFeatures != null
&& command.editedFeatures.containsKey(seq))
{
- sequence.setSequenceFeatures((SequenceFeature[]) command.editedFeatures
+ sequence.setSequenceFeatures(command.editedFeatures
.get(seq));
}
if (command.editedFeatures == null)
{
- command.editedFeatures = new Hashtable();
+ command.editedFeatures = new Hashtable<SequenceI, SequenceFeature[]>();
}
command.editedFeatures.put(seq, oldsf);
boolean fullAlignmentHeight = false;
- Hashtable deletedAnnotationRows;
+ Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
- Hashtable deletedAnnotations;
+ Hashtable<String, Annotation[]> deletedAnnotations;
- Hashtable editedFeatures;
+ Hashtable<SequenceI, SequenceFeature[]> editedFeatures;
AlignmentI al;
- int command;
+ Action command;
char[][] string;
char gapChar;
- Edit(int command, SequenceI[] seqs, int position, int number,
+ Edit(Action command, SequenceI[] seqs, int position, int number,
char gapChar)
{
this.command = command;
this.gapChar = gapChar;
}
- Edit(int command, SequenceI[] seqs, int position, int number,
+ Edit(Action command, SequenceI[] seqs, int position, int number,
AlignmentI al)
{
this.gapChar = al.getGapCharacter();
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
- Edit(int command, SequenceI[] seqs, int position, int number,
+ Edit(Action command, SequenceI[] seqs, int position, int number,
AlignmentI al, String replace)
{
this.command = command;
* Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
public class RemoveGapColCommand extends EditCommand
{
int startCol = -1, endCol = -1;
columnsDeleted = 0;
- edits = new Edit[0];
+ clearEdits();
boolean delete = true;
for (int i = start; i <= end; i++)
if (!delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, endCol
+ this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
+ endCol
- startCol, al, false, null);
columnsDeleted += (endCol - startCol);
// This is for empty columns at the
// end of the alignment
- this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, end
+ this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
+ end
- startCol + 1, al, false, null);
columnsDeleted += (end - startCol + 1);
* Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
public class RemoveGapsCommand extends EditCommand
{
int j, jSize;
- edits = new Edit[0];
+ clearEdits();
boolean delete = true;
char[] sequence;
if (!delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, new SequenceI[]
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[]
{ seqs[s] }, start + startCol - deletedCols, endCol - startCol,
al, false, null);
}
if (delete && startCol > -1)
{
- this.appendEdit(DELETE_GAP, new SequenceI[]
+ this.appendEdit(Action.DELETE_GAP, new SequenceI[]
{ seqs[s] }, start + startCol - deletedCols, jSize - startCol, al,
false, null);
}
*/
package jalview.commands;
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceI;
public class SlideSequencesCommand extends EditCommand
{
for (i = 0; i < lSize; i++)
{
for (j = 0; j < slideSize; j++)
+ {
if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))
{
gapsInsertedBegin = true;
break;
}
+ }
}
+ Edit e = null;
+
if (!gapsInsertedBegin)
- edits = new Edit[]
- { new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar) };
+ {
+ e = new Edit(Action.DELETE_GAP, seqsLeft, 0, slideSize, gapChar);
+ setEdit(e);
+ }
else
- edits = new Edit[]
- { new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar) };
+ {
+ e = new Edit(Action.INSERT_GAP, seqsRight, 0, slideSize, gapChar);
+ setEdit(e);
+ }
- performEdit(0, null);
+ performEdit(e, null);
}
public boolean getGapsInsertedBegin()
{
boolean same = false;
- if (command.edits[0].seqs.length == edits[0].seqs.length)
+ if (command.getEdit(0).seqs.length == getEdit(0).seqs.length)
{
same = true;
- for (int i = 0; i < command.edits[0].seqs.length; i++)
+ for (int i = 0; i < command.getEdit(0).seqs.length; i++)
{
- if (edits[0].seqs[i] != command.edits[0].seqs[i])
+ if (getEdit(0).seqs[i] != command.getEdit(0).seqs[i])
{
same = false;
}
if (same)
{
- Edit[] temp = new Edit[command.edits.length + 1];
- System.arraycopy(command.edits, 0, temp, 0, command.edits.length);
- command.edits = temp;
- command.edits[command.edits.length - 1] = edits[0];
+ command.addEdit(getEdit(0));
}
return same;
*/
package jalview.commands;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.ShiftList;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.util.List;
public class TrimRegionCommand extends EditCommand
{
SequenceGroup selectionGroup;
- Vector deletedHiddenColumns;
+ List<int[]> deletedHiddenColumns;
int columnsDeleted;
columnsDeleted = column;
- edits = new Edit[]
- { new Edit(CUT, seqs, 0, column, al) };
+ setEdit(new Edit(Action.CUT, seqs, 0, column, al));
}
else if (command.equalsIgnoreCase(TRIM_RIGHT))
{
columnsDeleted = width - 1;
- edits = new Edit[]
- { new Edit(CUT, seqs, column + 1, width, al) };
+ setEdit(new Edit(Action.CUT, seqs, column + 1, width, al));
}
// We need to keep a record of the sequence start
// in order to restore the state after a redo
- int i, isize = edits[0].seqs.length;
+ int i, isize = getEdit(0).seqs.length;
start = new int[isize];
for (i = 0; i < isize; i++)
{
- start[i] = edits[0].seqs[i].getStart();
+ start[i] = getEdit(0).seqs[i].getStart();
}
performEdit(0, null);
int[] region;
for (int i = 0; i < deletedHiddenColumns.size(); i++)
{
- region = (int[]) deletedHiddenColumns.elementAt(i);
+ region = deletedHiddenColumns.get(i);
colSel.hideColumns(region[0], region[1]);
}
}
public SequenceI[] getSequencesArray()
{
if (sequences == null)
+ {
return null;
+ }
synchronized (sequences)
{
return sequences.toArray(new SequenceI[sequences.size()]);
}
}
if (hiddenSequences != null)
+ {
hiddenSequences.adjustHeightSequenceAdded();
+ }
}
/**
public void finalize()
{
if (getDataset() != null)
+ {
getDataset().removeAlignmentRef();
+ }
dataset = null;
sequences = null;
continue;
}
if (tIndex < temp.length)
+ {
temp[tIndex++] = annotations[i];
+ }
}
if (swap)
else if (dataset == null && data != null)
{
dataset = data;
+ for (int i = 0; i < getHeight(); i++)
+ {
+ SequenceI currentSeq = getSequenceAt(i);
+ SequenceI dsq = currentSeq.getDatasetSequence();
+ if (dsq == null)
+ {
+ dsq = currentSeq.createDatasetSequence();
+ dataset.addSequence(dsq);
+ }
+ else
+ {
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ if (dataset.findIndex(dsq) == -1)
+ {
+ dataset.addSequence(dsq);
+ }
+ }
+ }
}
dataset.addAlignmentRef();
}
public void setProperty(Object key, Object value)
{
if (alignmentProperties == null)
+ {
alignmentProperties = new Hashtable();
+ }
alignmentProperties.put(key, value);
}
public Object getProperty(Object key)
{
if (alignmentProperties != null)
+ {
return alignmentProperties.get(key);
+ }
else
+ {
return null;
+ }
}
@Override
public void addCodonFrame(AlignedCodonFrame codons)
{
if (codons == null)
+ {
return;
+ }
if (codonFrameList == null)
{
codonFrameList = new AlignedCodonFrame[]
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
if (seq == null || codonFrameList == null)
+ {
return null;
+ }
Vector cframes = new Vector();
for (int f = 0; f < codonFrameList.length; f++)
{
if (codonFrameList[f].involvesSequence(seq))
+ {
cframes.addElement(codonFrameList[f]);
+ }
}
if (cframes.size() == 0)
+ {
return null;
+ }
AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
cframes.copyInto(cfr);
return cfr;
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
if (codons == null || codonFrameList == null)
+ {
return false;
+ }
boolean removed = false;
int i = 0, iSize = codonFrameList.length;
while (i < iSize)
public SequenceFeature[] _rnasecstr = null;
/**
- * position of annotation resulting in invalid WUSS parsing or -1
+ * position of annotation resulting in invalid WUSS parsing or -1. -2 means
+ * there was no RNA structure in this annotation
*/
- private long invalidrnastruc = -1;
+ private long invalidrnastruc = -2;
/**
* Updates the _rnasecstr field Determines the positions that base pair and
isrna = true;
showAllColLabels = true;
scaleColLabel = true;
+ _markRnaHelices();
}
// System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+
}
+ private void _markRnaHelices()
+ {
+ int mxval = 0;
+ // Figure out number of helices
+ // Length of rnasecstr is the number of pairs of positions that base pair
+ // with each other in the secondary structure
+ for (int x = 0; x < _rnasecstr.length; x++)
+ {
+
+ /*
+ * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+ * this.annotation._rnasecstr[x].getBegin());
+ */
+ // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+ int val = 0;
+ try
+ {
+ val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+ if (mxval < val)
+ {
+ mxval = val;
+ }
+ } catch (NumberFormatException q)
+ {
+ }
+ ;
+
+ annotations[_rnasecstr[x].getBegin()].value = val;
+ annotations[_rnasecstr[x].getEnd()].value = val;
+
+ // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+ // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+ }
+ setScore(mxval);
+ }
/**
* map of positions in the associated annotation
*/
@Override
public char charAt(int index)
{
- String dc;
return ((index + offset < 0) || (index + offset) >= max
- || annotations[index + offset] == null || (dc = annotations[index
- + offset].displayCharacter.trim()).length() < 1) ? '.' : dc
- .charAt(0);
+ || annotations[index + offset] == null || (annotations[index
+ + offset].secondaryStructure < ' ') ? ' '
+ : annotations[index + offset].secondaryStructure);
}
public String toString()
for (int i = offset; i < mx; i++)
{
- String dc;
- string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter
- .trim()).length() < 1) ? '.' : dc.charAt(0);
+ string[i] = (annotations[i] == null || (annotations[i].secondaryStructure < 32)) ? ' '
+ : annotations[i].secondaryStructure;
}
return new String(string);
}
*/
package jalview.datamodel;
-import java.util.*;
+import jalview.util.ShiftList;
-import jalview.util.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
/**
* NOTE: Columns are zero based.
* @param left
* shift in edit (+ve for removal, or -ve for inserts)
*/
- public Vector compensateForEdit(int start, int change)
+ public List<int[]> compensateForEdit(int start, int change)
{
- Vector deletedHiddenColumns = null;
+ List<int[]> deletedHiddenColumns = null;
for (int i = 0; i < size(); i++)
{
int temp = columnAt(i);
if (hiddenColumns != null)
{
- deletedHiddenColumns = new Vector();
+ deletedHiddenColumns = new ArrayList<int[]>();
int hSize = hiddenColumns.size();
for (int i = 0; i < hSize; i++)
{
int[] region = (int[]) hiddenColumns.elementAt(i);
if (region[0] > start && start + change > region[1])
{
- deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
+ deletedHiddenColumns.add(region);
hiddenColumns.removeElementAt(i);
i--;
public boolean isVisible(int column)
{
if (hiddenColumns != null)
+ {
for (int i = 0; i < hiddenColumns.size(); i++)
{
int[] region = (int[]) hiddenColumns.elementAt(i);
return false;
}
}
+ }
return true;
}
w += els.length;
}
if (w == 0)
+ {
return;
+ }
Enumeration e = annels.elements();
alignmentAnnotation.annotations = new Annotation[w];
w = 0;
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
public class HiddenSequences
{
alignment.deleteSequence(sequence);
}
- public Vector showAll(
+ public List<SequenceI> showAll(
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
for (int i = 0; i < hiddenSequences.length; i++)
{
if (hiddenSequences[i] != null)
{
- Vector tmp = showSequence(i, hiddenRepSequences);
- for (int t = 0; t < tmp.size(); t++)
+ List<SequenceI> tmp = showSequence(i, hiddenRepSequences);
+ for (SequenceI seq : tmp)
{
- revealedSeqs.addElement(tmp.elementAt(t));
+ revealedSeqs.add(seq);
}
}
}
return revealedSeqs;
}
- public Vector showSequence(int alignmentIndex,
+ public List<SequenceI> showSequence(int alignmentIndex,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
if (repSequence != null && hiddenRepSequences != null
&& hiddenRepSequences.containsKey(repSequence))
{
hiddenRepSequences.remove(repSequence);
- revealedSeqs.addElement(repSequence);
+ revealedSeqs.add(repSequence);
}
int start = adjustForHiddenSeqs(alignmentIndex - 1);
{
if (seq.getLength() > 0)
{
- revealedSeqs.addElement(seq);
+ revealedSeqs.add(seq);
asequences.add(alignmentIndex, seq);
}
else
seqs.add(sq);
if (!isNa)
{
+ String mt = model.getModelTitle() == null ? getDataName()
+ : model.getModelTitle();
+ mt += _lastChainId;
AlignmentAnnotation ann = new AlignmentAnnotation(
"Secondary Structure",
- "Secondary Structure from PDB File", asecstr);
+ "Secondary Structure for " + mt, asecstr);
ann.belowAlignment=true;
ann.visible=true;
ann.autoCalculated=false;
public void colourByChain()
{
colourBySequence = false;
- // this is not a valid Chimera command; is there one? Menu option hidden
- evalStateCommand("select *;color chain",false);
+ evalStateCommand("rainbow chain", false);
}
public void colourByCharge()
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
if (viewport.historyList.size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
+ CommandI command = viewport.historyList.peek();
undoMenuItem.setText(MessageManager.formatMessage(
"label.undo_command", new String[]
{ command.getDescription() }));
{
redoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.redoList.peek();
+ CommandI command = viewport.redoList.peek();
redoMenuItem.setText(MessageManager.formatMessage(
"label.redo_command", new String[]
{ command.getDescription() }));
{
return;
}
- CommandI command = (CommandI) viewport.historyList.pop();
+ CommandI command = viewport.historyList.pop();
viewport.redoList.push(command);
command.undoCommand(getViewAlignments());
return;
}
- CommandI command = (CommandI) viewport.redoList.pop();
+ CommandI command = viewport.redoList.pop();
viewport.historyList.push(command);
command.doCommand(getViewAlignments());
// /////
// ADD HISTORY ITEM
//
- addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE,
sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
viewport.setSelectionGroup(null);
aa.visible = visible;
}
}
- this.alignPanel.paintAlignment(true);
+ alignPanel.validateAnnotationDimensions(false);
+ alignPanel.alignmentChanged();
}
/**
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
boolean gatherViewsHere = false;
- Stack historyList = new Stack();
+ Stack<CommandI> historyList = new Stack<CommandI>();
- Stack redoList = new Stack();
+ Stack<CommandI> redoList = new Stack<CommandI>();
int thresholdTextColour = 0;
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
}
initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
{
desc.append("<br/>");
}
-
+ // if (aa.hasProperties())
+ // {
+ // desc.append("<table>");
+ // for (String prop : aa.getProperties())
+ // {
+ // desc.append("<tr><td>" + prop + "</td><td>"
+ // + aa.getProperty(prop) + "</td><tr>");
+ // }
+ // desc.append("</table>");
+ // }
}
else
{
// begin the tooltip's html fragment
desc.append("<html>");
+ if (aa.hasScore())
+ {
+ // TODO: limit precision of score to avoid noise from imprecise
+ // doubles
+ // (64.7 becomes 64.7+/some tiny value).
+ desc.append(" Score: " + aa.score);
+ }
}
- if (aa.hasScore())
- {
- // TODO: limit precision of score to avoid noise from imprecise doubles
- // (64.7 becomes 64.7+/some tiny value).
- desc.append(" Score: " + aa.score);
- }
-
if (desc.length() > 6)
{
desc.append("</html>");
this.setToolTipText(null);
}
}
-
}
/**
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
import jalview.util.MessageManager;
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JColorChooser;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.Scrollable;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
/**
* AnnotationPanel displays visible portion of annotation rows below unwrapped
* alignment
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
int index = av.getColumnSelection().columnAt(i);
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", type, 0);
}
- anot[index].secondaryStructure = type;
+
+ anot[index].secondaryStructure = type != 'S' ? type : label
+ .length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
}
int index = columnSelection.columnAt(i);
// always check for current display state - just in case
if (!viscols.isVisible(index))
+ {
continue;
+ }
String tlabel = null;
if (anot[index] != null)
{ // LML added stem code
}
imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
if (imgWidth < 1)
+ {
return;
+ }
if (image == null || imgWidth != image.getWidth(this)
|| image.getHeight(this) != getHeight())
{
return bounds;
}
else
+ {
return null;
+ }
}
}
_alignwith = new Vector<AlignmentPanel>();
}
- // no colour by chain command in Chimera?
- chainColour.setVisible(false);
-
// save As not yet implemented
savemenu.setVisible(false);
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.structure.StructureSelectionManager;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.ws.params.ParamManager;
instance = this;
doVamsasClientCheck();
doGroovyCheck();
-
+ doConfigureStructurePrefs();
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
}
jconsole = new Console(this, showjconsole);
// add essential build information
- jconsole.setHeader("Jalview Desktop "
+ jconsole.setHeader("Jalview Version: "
+ jalview.bin.Cache.getProperty("VERSION") + "\n"
+ + "Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
+ + "\n"
+ "Build Date: "
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+ "Java version: " + System.getProperty("java.version") + "\n"
});
}
+ public void doConfigureStructurePrefs()
+ {
+ // configure services
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(this);
+ if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
+ {
+ ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
+ Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+ ssm.setSecStructServices(jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW,
+ true));
+ }
+ else
+ {
+ ssm.setAddTempFacAnnot(false);
+ ssm.setProcessSecondaryStructure(false);
+ ssm.setSecStructServices(false);
+ }
+ }
+
public void checkForNews()
{
final Desktop me = this;
+ ermsg
+ "</td></tr></table>"
+ "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
- + " or mis-configured HTTP proxy settings.</p>"
+ + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+ "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ " Tools->Preferences dialog box to change them.</p></html>"),
"Web Service Configuration Problem",
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.GraduatedColor;
import java.util.List;
import java.util.Vector;
+import javax.help.HelpSetException;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
import javax.swing.Icon;
ex.printStackTrace();
}
- table = new JTable();
+ table = new JTable() {
+ @Override
+ public String getToolTipText(MouseEvent e) {
+ if (table.columnAtPoint(e.getPoint()) == 0) {
+ /*
+ * Tooltip for feature name only
+ */
+ return JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.feature_settings_click_drag"));
+ }
+ return null;
+ }
+ };
table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
table.setFont(new Font("Verdana", Font.PLAIN, 12));
table.setDefaultRenderer(Color.class, new ColorRenderer());
}
}
});
- table.setToolTipText(JvSwingUtils
- .wrapTooltip(true, MessageManager.getString("label.feature_settings_click_drag")));
+// table.setToolTipText(JvSwingUtils.wrapTooltip(true,
+// MessageManager.getString("label.feature_settings_click_drag")));
scrollPane.setViewportView(table);
dassourceBrowser = new DasSourceBrowser(this);
|| ((Boolean) fr.featureGroups.get(group)).booleanValue())
{
if (group != null)
+ {
checkGroupState(group);
+ }
type = tmpfeatures[index].getType();
if (!visibleChecks.contains(type))
{
if (fr.renderOrder != null)
{
if (!handlingUpdate)
+ {
fr.findAllFeatures(groupChanged != null); // prod to update
+ }
// colourschemes. but don't
// affect display
// First add the checks in the previous render order,
{
order[i] = fr.getOrder(data[i][0].toString());
if (order[i] < 0)
+ {
order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
+ }
if (i > 1)
+ {
sort = sort || order[i - 1] > order[i];
+ }
}
if (sort)
+ {
jalview.util.QuickSort.sort(order, data);
+ }
}
void load()
public void orderByAvWidth()
{
if (table == null || table.getModel() == null)
+ {
return;
+ }
Object[][] data = ((FeatureTableModel) table.getModel()).getData();
float[] width = new float[data.length];
float[] awidth;
width[i] = 0;
}
if (max < width[i])
+ {
max = width[i];
+ }
}
boolean sort = false;
for (int i = 0; i < width.length; i++)
fr.setOrder(data[i][0].toString(), width[i]); // store for later
}
if (i > 0)
+ {
sort = sort || width[i - 1] > width[i];
+ }
}
if (sort)
+ {
jalview.util.QuickSort.sort(width, data);
// update global priority order
+ }
updateFeatureRenderer(data, false);
table.repaint();
JButton sortByDens = new JButton();
- JPanel transbuttons = new JPanel(new GridLayout(4, 1));
+ JButton help = new JButton();
+
+ JPanel transbuttons = new JPanel(new GridLayout(5, 1));
private void jbInit() throws Exception
{
sortByDens(null);
}
});
+ help.setFont(JvSwingUtils.getLabelFont());
+ help.setText(MessageManager.getString("action.help"));
+ help.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.SequenceFeatureSettings);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
cancel.setFont(JvSwingUtils.getLabelFont());
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
});
transparency.setMaximum(70);
+ transparency.setToolTipText(MessageManager
+ .getString("label.transparency_tip"));
fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
fetchDAS.addActionListener(new ActionListener()
{
transbuttons.add(invert);
transbuttons.add(sortByScore);
transbuttons.add(sortByDens);
+ transbuttons.add(help);
+ JPanel sliderPanel = new JPanel();
+ sliderPanel.add(transparency);
transPanel.add(transparency);
transPanel.add(transbuttons);
buttonPanel.add(ok);
import java.net.URL;
+import javax.help.BadIDException;
import javax.help.HelpBroker;
import javax.help.HelpSet;
import javax.help.HelpSetException;
*/
public class Help
{
+ public enum HelpId
+ {
+ Home("home"), SequenceFeatureSettings("seqfeatures.settings");
+
+ private String id;
+
+ private HelpId(String loc)
+ {
+ this.id = loc;
+ }
+
+ @Override
+ public String toString()
+ {
+ return this.id;
+ }
+ }
private static final long HALF_A_MO = 500; // half a second
*
* This is a workaround for issue JAL-914 - both Desktop and AlignFrame
* responding to F1 key, resulting in duplicate help windows opened.
+ * @param id TODO
*
* @throws HelpSetException
*/
- public static void showHelpWindow() throws HelpSetException
+ public static void showHelpWindow(HelpId id) throws HelpSetException
{
long timeNow = System.currentTimeMillis();
HelpSet hs = new HelpSet(cl, url);
HelpBroker hb = hs.createHelpBroker();
- hb.setCurrentID("home");
+ try
+ {
+ hb.setCurrentID(id.toString());
+ } catch (BadIDException bad)
+ {
+ System.out.println("Bad help link: " + id.toString()
+ + ": must match a target in help.jhm");
+ throw bad;
+ }
hb.setDisplayed(true);
}
}
+
+ public static void showHelpWindow() throws HelpSetException
+ {
+ showHelpWindow(HelpId.Home);
+ }
}
import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
{
AlignmentAnnotation[] aa = ap.av.getAlignment()
.getAlignmentAnnotation();
- for (int i = 0; i < aa.length; i++)
+ for (int i = 0; aa != null && i < aa.length; i++)
{
- if (aa[i].getRNAStruc() != null)
+ if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
{
final String rnastruc = aa[i].getRNAStruc();
- final String structureLine = aa[i].label;
+ final String structureLine = aa[i].label + " (alignment)";
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
"label.2d_rna_structure_line", new String[]
@Override
public void actionPerformed(ActionEvent e)
{
- // System.out.println("1:"+structureLine);
- System.out.println("1:sname" + seq.getName());
- System.out.println("2:seq" + seq);
-
- // System.out.println("3:"+seq.getSequenceAsString());
- System.out.println("3:strucseq" + rnastruc);
- // System.out.println("4:struc"+seq.getRNA());
- System.out.println("5:name" + seq.getName());
- System.out.println("6:ap" + ap);
+ // // System.out.println("1:"+structureLine);
+ // System.out.println("1:sname" + seq.getName());
+ // System.out.println("2:seq" + seq);
+ //
+ // // System.out.println("3:"+seq.getSequenceAsString());
+ // System.out.println("3:strucseq" + rnastruc);
+ // // System.out.println("4:struc"+seq.getRNA());
+ // System.out.println("5:name" + seq.getName());
+ // System.out.println("6:ap" + ap);
new AppVarna(structureLine, seq, seq.getSequenceAsString(),
rnastruc, seq.getName(), ap);
// new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
AlignmentAnnotation seqAnno[] = seq.getAnnotation();
for (int i = 0; i < seqAnno.length; i++)
{
- if (seqAnno[i].getRNAStruc() != null)
+ if (seqAnno[i].isValidStruc())
{
final String rnastruc = seqAnno[i].getRNAStruc();
{
EditCommand editCommand = new EditCommand(
MessageManager.getString("label.edit_sequences"),
- EditCommand.REPLACE, dialog.getName().replace(' ',
+ Action.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
@Override
public void actionPerformed(ActionEvent e)
{
- if (chimeraPath.getText().trim().length() > 0)
- {
- File f = new File(chimeraPath.getText());
- if (!f.canExecute())
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.invalid_path"),
- MessageManager.getString("label.invalid_name"),
- JOptionPane.ERROR_MESSAGE);
- }
- }
+ validateChimeraPath();
}
});
*/
public void ok_actionPerformed(ActionEvent e)
{
+ if (!validateSettings())
+ {
+ return;
+ }
+
/*
* Save Visual settings
*/
dasSource.saveProperties(Cache.applicationProperties);
wsPrefs.updateAndRefreshWsMenuConfig(false);
-
Cache.saveProperties();
-
+ Desktop.instance.doConfigureStructurePrefs();
try
{
frame.setClosed(true);
}
/**
+ * Do any necessary validation before saving settings.
+ *
+ * @return
+ */
+ private boolean validateSettings()
+ {
+ if (!validateStructure())
+ {
+ structureTab.requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ protected boolean validateStructure()
+ {
+ return validateChimeraPath();
+
+ }
+ /**
* DOCUMENT ME!
*/
public void startupFileTextfield_mouseClicked()
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
}
+ /**
+ * Returns true if chimera path is to a valid executable, else show an error
+ * dialog.
+ */
+ private boolean validateChimeraPath()
+ {
+ if (chimeraPath.getText().trim().length() > 0)
+ {
+ File f = new File(chimeraPath.getText());
+ if (!f.canExecute())
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.invalid_chimera_path"),
+ MessageManager.getString("label.invalid_name"),
+ JOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+ }
+ return true;
+ }
+
}
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GSliderPanel;
import jalview.util.MessageManager;
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JProgressBar;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
/**
* DOCUMENT ME!
*
AlignmentPanel ap;
- Stack historyList = new Stack(); // simpler than synching with alignFrame.
+ Stack<CommandI> historyList = new Stack<CommandI>();
+
+ // simpler than synching with alignFrame.
float[] redundancy;
}
EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),
- EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
+ Action.CUT, deleted, 0, width, ap.av.getAlignment());
for (int i = 0; i < del.size(); i++)
{
return;
}
- CommandI command = (CommandI) historyList.pop();
+ CommandI command = historyList.pop();
if (ap.av.historyList.contains(command))
{
command.undoCommand(af.getViewAlignments());
--- /dev/null
+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+
+public class SVGOptions extends JPanel
+{
+ JDialog dialog;
+
+ public boolean cancelled = false;
+
+ String value;
+
+ public SVGOptions()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ ButtonGroup bg = new ButtonGroup();
+ bg.add(lineart);
+ bg.add(text);
+
+ JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
+ JOptionPane.DEFAULT_OPTION, null, new Object[]
+ { this });
+
+ dialog = pane.createDialog(Desktop.desktop, "SVG Rendering options");
+ dialog.setVisible(true);
+
+ }
+
+ private void jbInit() throws Exception
+ {
+ lineart.setFont(JvSwingUtils.getLabelFont());
+ lineart.setText(MessageManager.getString("label.lineart"));
+ text.setFont(JvSwingUtils.getLabelFont());
+ text.setText(MessageManager.getString("action.text"));
+ text.setSelected(true);
+ askAgain.setFont(JvSwingUtils.getLabelFont());
+ askAgain.setText(MessageManager.getString("label.dont_ask_me_again"));
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+ jLabel1.setFont(JvSwingUtils.getLabelFont());
+ jLabel1.setText("Select SVG character rendering style");
+ this.setLayout(borderLayout1);
+ jPanel3.setBorder(BorderFactory.createEtchedBorder());
+ jPanel2.add(text);
+ jPanel2.add(lineart);
+ jPanel2.add(askAgain);
+ jPanel1.add(ok);
+ jPanel1.add(cancel);
+ jPanel3.add(jLabel1);
+ jPanel3.add(jPanel2);
+ this.add(jPanel3, java.awt.BorderLayout.CENTER);
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ }
+
+ JRadioButton lineart = new JRadioButton();
+
+ JRadioButton text = new JRadioButton();
+
+ JCheckBox askAgain = new JCheckBox();
+
+ JButton ok = new JButton();
+
+ JButton cancel = new JButton();
+
+ JPanel jPanel1 = new JPanel();
+
+ JLabel jLabel1 = new JLabel();
+
+ JPanel jPanel2 = new JPanel();
+
+ JPanel jPanel3 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ if (lineart.isSelected())
+ {
+ value = "Lineart";
+ }
+ else
+ {
+ value = "Text";
+ }
+
+ if (!askAgain.isSelected())
+ {
+ jalview.bin.Cache.applicationProperties.remove("SVG_RENDERING");
+ }
+ else
+ {
+ jalview.bin.Cache.setProperty("SVG_RENDERING", value);
+ }
+
+ dialog.setVisible(false);
+ }
+
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ cancelled = true;
+ dialog.setVisible(false);
+ }
+
+ public String getValue()
+ {
+ return value;
+ }
+}
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.awt.BasicStroke;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JComponent;
/**
* DOCUMENT ME!
*/
public void fastPaint(int horizontal, int vertical)
{
- if (fastpainting)
+ if (fastpainting || gg == null)
{
return;
}
fastpainting = true;
- if (gg == null)
- {
- return;
- }
-
fastPaint = true;
gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
annotations = new AnnotationPanel(av);
}
- annotations.renderer.drawComponent(annotations, av, (Graphics2D) g,
+ annotations.renderer.drawComponent(annotations, av, g,
-1, startRes, endx + 1);
g.translate(0, -cHeight - ypos - 3);
}
if ((group == null) && (av.getAlignment().getGroups().size() > 0))
{
- group = (SequenceGroup) av.getAlignment().getGroups().get(0);
+ group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
}
break;
}
- group = (SequenceGroup) av.getAlignment().getGroups()
+ group = av.getAlignment().getGroups()
.get(groupIndex);
} while (groupIndex < av.getAlignment().getGroups().size());
package jalview.gui;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
startres, startres - lastres, av.getAlignment(), true);
}
}
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
startres, lastres - startres, av.getAlignment(), true);
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+ editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
{ seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
if (max > 0)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
+ editCommand.appendEdit(Action.DELETE_GAP,
new SequenceI[]
{ seq }, startres, max, av.getAlignment(), true);
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
+ editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[]
{ seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+ editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
av.getAlignment(), true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
+ editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
av.getAlignment(), true);
}
protected void revert_actionPerformed(ActionEvent e)
{
reInitDialog(lastParmSet);
-
+ updateWebServiceMenus();
}
protected void update_actionPerformed(ActionEvent e)
_deleteUserPreset(lastParmSet);
}
reInitDialog(null); // service default
+ updateWebServiceMenus();
}
protected void create_actionPerformed(ActionEvent e)
_storeCurrentPreset(curname);
lastParmSet = curname;
isUserPreset = true;
+ reInitDialog(curname);
initArgSetModified();
+ updateWebServiceMenus();
}
else
{
{
Vector<String> services = new Vector<String>();
services.addElement(args[p++]);
- Jws2Discoverer.setServiceUrls(services);
+ Jws2Discoverer.getDiscoverer().setServiceUrls(services);
}
try
{
SetNamePanel.validate();
validate();
settingDialog = false;
+ }
+ /**
+ * Rebuild the AlignFrame web service menus (after add/delete of a preset
+ * option).
+ */
+ protected void updateWebServiceMenus()
+ {
+ for (AlignFrame alignFrame : Desktop.getAlignframes())
+ {
+ alignFrame.BuildWebServiceMenu();
+ }
}
String curSetName = null;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.net.URL;
+import java.util.List;
import java.util.Vector;
import javax.swing.JLabel;
initFromPreferences();
}
- Vector<String> wsUrls, oldUrls, rsbsUrls, oldRsbsUrls;
+ List<String> wsUrls;
+
+ Vector<String> oldUrls, rsbsUrls, oldRsbsUrls;
private boolean needWsMenuUpdate;
private void initFromPreferences()
{
- wsUrls = jalview.ws.jws2.Jws2Discoverer.getServiceUrls();
- if (wsUrls != null)
+ wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
+ if (!wsUrls.isEmpty())
{
oldUrls = new Vector<String>(wsUrls);
}
private void updateServiceList()
{
- jalview.ws.jws2.Jws2Discoverer.setServiceUrls(wsUrls);
+ Jws2Discoverer.getDiscoverer().setServiceUrls(wsUrls);
}
private void updateRsbsServiceList()
int sel = wsList.getSelectedRow();
if (sel > -1)
{
- wsUrls.removeElementAt(sel);
+ wsUrls.remove(sel);
update++;
updateList();
}
int sel = wsList.getSelectedRow();
if (sel > -1)
{
- String url = editUrl(wsUrls.elementAt(sel), MessageManager.getString("label.edit_jabaws_url"));
+ String url = editUrl(wsUrls.get(sel),
+ MessageManager.getString("label.edit_jabaws_url"));
if (url != null)
{
int present = wsUrls.indexOf(url);
if (present == -1)
{
update++;
- wsUrls.setElementAt(url, sel);
+ wsUrls.set(sel, url);
updateList();
}
else
{
if (present != sel)
{
- wsUrls.removeElementAt(sel);
+ wsUrls.remove(sel);
updateList();
}
}
if (p > -1 && p < wsUrls.size() - 1)
{
String t = wsUrls.get(p + 1);
- wsUrls.setElementAt(wsUrls.elementAt(p), p + 1);
- wsUrls.setElementAt(t, p);
+ wsUrls.set(p + 1, wsUrls.get(p));
+ wsUrls.set(p, t);
updateList();
wsList.getSelectionModel().setSelectionInterval(p + 1, p + 1);
update++;
if (p > 0)
{
String t = wsUrls.get(p - 1);
- wsUrls.setElementAt(wsUrls.elementAt(p), p - 1);
- wsUrls.setElementAt(t, p);
+ wsUrls.set(p - 1, wsUrls.get(p));
+ wsUrls.set(p, t);
updateList();
wsList.getSelectionModel().setSelectionInterval(p - 1, p - 1);
update++;
if (validate == JOptionPane.OK_OPTION)
{
- if (jalview.ws.jws2.Jws2Discoverer.testServiceUrl(foo))
+ if (Jws2Discoverer.testServiceUrl(foo))
{
return foo.toString();
}
int selind = wsList.getSelectedRow();
if (selind > -1)
{
- wsUrls.insertElementAt(url, selind);
+ wsUrls.add(selind, url);
}
else
{
- wsUrls.addElement(url);
+ wsUrls.add(url);
}
update++;
updateList();
@Override
protected void resetWs_actionPerformed(ActionEvent e)
{
- jalview.ws.jws2.Jws2Discoverer.setServiceUrls(null);
- Vector nwsUrls = jalview.ws.jws2.Jws2Discoverer.getServiceUrls();
+ Jws2Discoverer.getDiscoverer().setServiceUrls(null);
+ List<String> nwsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
if (!wsUrls.equals(nwsUrls))
{
update++;
public static String CLASSLOADER = "ClassLoader";
+ /**
+ * add jalview-derived non-secondary structure annotation from PDB structure
+ */
+ boolean annotFromStructure = false;
+
+ /**
+ * add secondary structure from PDB data with built-in algorithms
+ */
+ boolean localSecondaryStruct = false;
+
+ /**
+ * process PDB data with web services
+ */
+ boolean serviceSecondaryStruct = false;
+
AlignFile afile = null;
String inFile;
}
else if (format.equals("PDB"))
{
- afile = new MCview.PDBfile(true,true,inFile, type);
+ afile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, inFile, type);
// Uncomment to test Jmol data based PDB processing: JAL-1213
// afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
}
}
else if (format.equals("PDB"))
{
- afile = new MCview.PDBfile(true,true,source);
+ afile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, source);
}
else if (format.equals("STH"))
{
package jalview.io;
import jalview.api.AlignViewportI;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
/**
* Additional formatting methods used by the application in a number of places.
public class FormatAdapter extends AppletFormatAdapter
{
+ public FormatAdapter()
+ {
+ super();
+ if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ {
+ annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ true);
+ localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ true);
+ serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ true);
+ }
+ else
+ {
+ // disable all PDB annotation options
+ annotFromStructure = false;
+ localSecondaryStruct = false;
+ serviceSecondaryStruct = false;
+ }
+ }
public String formatSequences(String format, SequenceI[] seqs,
String[] omitHiddenColumns)
{
public boolean getCacheSuffixDefault(String format)
{
if (isValidFormat(format))
+ {
return jalview.bin.Cache.getDefault(format.toUpperCase()
+ "_JVSUFFIX", true);
+ }
return false;
}
*/
package jalview.io;
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.ArrayList;
-
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import com.stevesoft.pat.Regex;
+
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
int end = seq.length();
id = current.getName();
+ if (id == null || id.trim().length() == 0)
+ {
+ id = safeName(getDataName());
+ if (result.size() > 1)
+ {
+ id += "." + i;
+ }
+ }
seqs[i] = new Sequence(id, seq, begin, end);
seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
annot[k]).charAt(0), 0f);
}
- AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
- current.getID(), ann);
+ AlignmentAnnotation align = new AlignmentAnnotation(
+ "Secondary Structure",
+ current.getID().trim().length() > 0 ? "Secondary Structure for "
+ + current.getID()
+ : "", ann);
seqs[i].addAlignmentAnnotation(align);
seqs[i].setRNA(result.get(i));
private String safeName(String dataName)
{
int b = 0;
- while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ if ((b = dataName.lastIndexOf(".")) > 0)
{
- dataName = dataName.substring(b + 1).trim();
-
+ dataName = dataName.substring(0, b - 1);
+ }
+ b = 0;
+ Regex m = new Regex("[\\/]?([-A-Za-z0-9]+)\\.?");
+ String mm = dataName;
+ while (m.searchFrom(dataName, b))
+ {
+ mm = m.stringMatched();
+ b = m.matchedTo();
}
- int e = (dataName.length() - dataName.indexOf(".")) + 1;
- dataName = dataName.substring(1, e).trim();
- return dataName;
+ return mm;
}
}
*/
package jalview.io;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- Hashtable seqs = new Hashtable();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
r = new Regex("# STOCKHOLM ([\\d\\.]+)");
if (!r.search(nextLine()))
{
- throw new IOException(MessageManager.getString("exception.stockholm_invalid_format"));
+ throw new IOException(
+ MessageManager
+ .getString("exception.stockholm_invalid_format"));
}
else
{
}
}
// logger.debug("Number of sequences: " + this.noSeqs);
- Enumeration accs = seqs.keys();
- while (accs.hasMoreElements())
+ for (Map.Entry<String, String> skey : seqs.entrySet())
{
- String acc = (String) accs.nextElement();
// logger.debug("Processing sequence " + acc);
- String seq = (String) seqs.remove(acc);
+ String acc = skey.getKey();
+ String seq = skey.getValue();
if (maxLength < seq.length())
{
maxLength = seq.length();
AlignmentAnnotation an = (AlignmentAnnotation) vv
.elementAt(ii);
seqO.addAlignmentAnnotation(an);
+ annotations.add(an);
}
}
}
if (!x.search(line))
{
// logger.error("Could not parse sequence line: " + line);
- throw new IOException(MessageManager.formatMessage("exception.couldnt_parse_sequence_line", new String[]{line}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.couldnt_parse_sequence_line", new String[]
+ { line }));
}
- String ns = (String) seqs.get(x.stringMatched(1));
+ String ns = seqs.get(x.stringMatched(1));
if (ns == null)
{
ns = "";
}
else
{
- throw new IOException(MessageManager.formatMessage("exception.error_parsing_line", new String[]{line}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.error_parsing_line", new String[]
+ { line }));
}
}
else if (annType.equals("GC"))
strucAnn = new Hashtable();
}
- Vector newStruc = new Vector();
+ Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
parseAnnotationRow(newStruc, type, ns);
-
+ for (AlignmentAnnotation alan : newStruc)
+ {
+ alan.visible = false;
+ }
+ // annotations.addAll(newStruc);
strucAnn.put(type, newStruc);
seqAnn.put(acc, strucAnn);
}
}
else
{
- throw new IOException(MessageManager.formatMessage("exception.unknown_annotation_detected", new String[]{annType,annContent}));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.unknown_annotation_detected", new String[]
+ { annType, annContent }));
}
}
}
// be written out
if (ss)
{
- if (detectbrackets.search(pos))
- {
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getRNASecStrucState(pos).charAt(0);
- }
- else
+ //if (" .-_".indexOf(pos) == -1)
{
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getDssp3state(pos).charAt(0);
- }
+ if (detectbrackets.search(pos))
+ {
+ ann.secondaryStructure = jalview.schemes.ResidueProperties
+ .getRNASecStrucState(pos).charAt(0);
+ }
+ else
+ {
+ ann.secondaryStructure = jalview.schemes.ResidueProperties
+ .getDssp3state(pos).charAt(0);
+ }
- if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
- {
- ann.displayCharacter = ""; // null; // " ";
- }
- else
- {
- ann.displayCharacter = " " + ann.displayCharacter;
+ if (ann.secondaryStructure == pos.charAt(0))
+ {
+ ann.displayCharacter = ""; // null; // " ";
+ }
+ else
+ {
+ ann.displayCharacter = " " + ann.displayCharacter;
+ }
}
+
}
els[i] = ann;
{
annot = (AlignmentAnnotation) e.nextElement();
if (annot.label.equals(type))
+ {
break;
+ }
annot = null;
}
if (annot == null)
for (int idb = 0; idb < s[in].getDBRef().length; idb++)
{
if (dataRef == null)
+ {
dataRef = new Hashtable();
+ }
String datAs1 = s[in].getDBRef()[idb].getSource().toString()
+ " ; "
String key = type2id(feature);
if (key == null)
+ {
continue;
+ }
// out.append("#=GR ");
out.append(new Format("%-" + maxid + "s").form("#=GR "
+ printId(s[i]) + " " + key + " "));
ann = alAnot[j].annotations;
+ boolean isrna = alAnot[j].isValidStruc();
String seq = "";
for (int k = 0; k < ann.length; k++)
{
- annot = ann[k];
- String ch = (annot == null) ? Character.toString(s[i]
- .getCharAt(k)) : annot.displayCharacter;
- if (ch.length() == 0)
- {
- if (key.equals("SS"))
- {
- char ll = annot.secondaryStructure;
- seq = (Character.toString(ll).equals(" ")) ? seq + "C"
- : seq + ll;
- }
- else
- {
- seq += ".";
- }
- }
- else if (ch.length() == 1)
- {
- seq += ch;
- }
- else if (ch.length() > 1)
- {
- seq += ch.charAt(1);
- }
+ seq += outputCharacter(key, k, isrna, ann, s[i]);
}
out.append(seq);
out.append(newline);
for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
{
aa = al.getAlignmentAnnotation()[ia];
- if (aa.autoCalculated || !aa.visible)
+ if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
{
continue;
}
String seq = "";
String label;
-
+ String key = "";
if (aa.label.equals("seq"))
+ {
label = "seq_cons";
+ }
else
- label = type2id(aa.label.toLowerCase()) + "_cons";
+ {
+ label = (key = type2id(aa.label.toLowerCase())) + "_cons";
+ }
if (label == null)
+ {
label = aa.label;
+ }
out.append(new Format("%-" + maxid + "s").form("#=GC " + label
+ " "));
+ boolean isrna = aa.isValidStruc();
for (int j = 0; j < aa.annotations.length; j++)
{
- String ch = (aa.annotations[j] == null) ? "-"
- : aa.annotations[j].displayCharacter;
- if (ch.length() == 0)
- {
- char ll = aa.annotations[j].secondaryStructure;
- if (Character.toString(ll).equals(" "))
- seq += "C";
- else
- seq += ll;
- }
- else if (ch.length() == 1)
- {
- seq += ch;
- }
- else if (ch.length() > 1)
- {
- seq += ch.charAt(1);
- }
+ seq += outputCharacter(key, j, isrna, aa.annotations, null);
}
out.append(seq);
out.append(newline);
return out.toString();
}
+ /**
+ * add an annotation character to the output row
+ *
+ * @param seq
+ * @param key
+ * @param k
+ * @param isrna
+ * @param ann
+ * @param sequenceI
+ */
+ private char outputCharacter(String key, int k,
+ boolean isrna, Annotation[] ann, SequenceI sequenceI)
+ {
+ char seq = ' ';
+ Annotation annot = ann[k];
+ String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
+ .toString(sequenceI.getCharAt(k)))
+ : annot.displayCharacter;
+ if (key.equals("SS"))
+ {
+ if (annot == null)
+ {
+ // sensible gap character if one is available or make one up
+ return sequenceI == null ? '-' : sequenceI
+ .getCharAt(k);
+ }
+ else
+ {
+ // valid secondary structure AND no alternative label (e.g. ' B')
+ if (annot.secondaryStructure > ' ' && ch.length() < 2)
+ {
+ return annot.secondaryStructure;
+ }
+ }
+ }
+
+ if (ch.length() == 0)
+ {
+ seq = '.';
+ }
+ else if (ch.length() == 1)
+ {
+ seq = ch.charAt(0);
+ }
+ else if (ch.length() > 1)
+ {
+ seq = ch.charAt(1);
+ }
+ return seq;
+ }
+
public String print()
{
out = new StringBuffer();
}
if (key != null)
{
- return (String) key;
+ return key;
}
System.err.println("Warning : Unknown Stockholm annotation type: "
+ type);
sortByAnnotScore.setText(MessageManager
.getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
- sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+ sort.addMenuListener(new javax.swing.event.MenuListener()
{
@Override
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Component;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
+import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
import javax.swing.border.TitledBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
protected JCheckBox showNpTooltip = new JCheckBox();
/*
- * Annotations tab components
+ * Structure tab and components
*/
+ protected JPanel structureTab;
+
protected JCheckBox structFromPdb = new JCheckBox();
protected JCheckBox useRnaView = new JCheckBox();
*/
private void jbInit() throws Exception
{
- JTabbedPane tabbedPane = new JTabbedPane();
+ final JTabbedPane tabbedPane = new JTabbedPane();
this.setLayout(new BorderLayout());
JPanel okCancelPanel = initOkCancelPanel();
this.add(tabbedPane, BorderLayout.CENTER);
*/
wsTab.setLayout(new BorderLayout());
tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+
+ /*
+ * Handler to validate a tab before leaving it - currently only for
+ * Structure.
+ */
+ tabbedPane.addChangeListener(new ChangeListener()
+ {
+ private Component lastTab;
+
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+ if (lastTab == structureTab
+ && tabbedPane.getSelectedComponent() != structureTab)
+ {
+ if (!validateStructure())
+ {
+ tabbedPane.setSelectedComponent(structureTab);
+ return;
+ }
+ }
+ lastTab = tabbedPane.getSelectedComponent();
+ }
+
+ });
}
/**
*/
private JPanel initStructureTab()
{
- JPanel structureTab = new JPanel();
+ structureTab = new JPanel();
+
structureTab.setBorder(new TitledBorder(MessageManager
.getString("label.structure_options")));
structureTab.setLayout(null);
pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
pathLabel.setText(MessageManager.getString("label.chimera_path"));
- pathLabel.setToolTipText(MessageManager
- .getString("label.chimera_path_tip"));
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_path_tip"));
+ pathLabel.setToolTipText(tooltip);
pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
structureTab.add(pathLabel);
chimeraPath.setFont(verdana11);
chimeraPath.setText("");
chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
+ chimeraPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser();
+ if (chosen != null)
+ {
+ chimeraPath.setText(chosen);
+ }
+ }
+ }
+ });
structureTab.add(chimeraPath);
return structureTab;
}
/**
+ * Show a dialog for the user to choose a file. Returns the chosen path, or
+ * null on Cancel.
+ *
+ * @return
+ */
+ protected String openFileChooser()
+ {
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+
+ // chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager
+ .getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
+ /**
+ * Validate the structure tab preferences; if invalid, set focus on this tab.
+ *
+ * @param e
+ */
+ protected boolean validateStructure(FocusEvent e)
+ {
+ if (!validateStructure())
+ {
+ e.getComponent().requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ protected boolean validateStructure()
+ {
+ return false;
+ }
+
+ /**
* Initialises the Visual tabbed panel.
*
* @return
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
import java.awt.BasicStroke;
import java.awt.Color;
int x2 = (x * charWidth);
Regex closeparen = new Regex("(\\))");
- String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
- : row_annotations[column - 1].displayCharacter;
+ char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
+ : row_annotations[column - 1].secondaryStructure;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+ || dc != row_annotations[sCol - 1].secondaryStructure;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
- || !dc.equals(row_annotations[column].displayCharacter);
+ || dc != row_annotations[column].secondaryStructure;
// System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
- if (column > 0 && closeparen.search(dc))
+ if (column > 0 && ResidueProperties.isCloseParenRNA(dc))
{
if (diffupstream)
}
}
}
- if (!row.isValidStruc())
+ if (row.getInvalidStrucPos() > x)
{
g.setColor(Color.orange);
- g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
- charWidth, charHeight);
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
+ }
+ else if (row.getInvalidStrucPos() == x)
+ {
+ g.setColor(Color.orange.darker());
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
}
if (validCharWidth
&& validRes
charOffset = (int) ((charWidth - fmWidth) / 2f);
if (row_annotations[column].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(row_annotations[column].colour);
+ }
if (column == 0 || row.graph > 0)
{
}
if (aa_annotations[column].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(aa_annotations[column].colour);
+ }
y1 = y
- (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
continue;
}
if (aa_annotations[column].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(aa_annotations[column].colour);
+ }
y1 = y
- (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
if (aa_annotations[j] != null)
{
if (aa_annotations[j].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(aa_annotations[j].colour);
+ }
height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
if (height > y)
private boolean predefinedColours = false;
private boolean seqAssociated = false;
-
/**
* false if the scheme was constructed without a minColour and maxColour used
* to decide if existing colours should be taken from annotation elements when
bb = maxColour.getBlue() - b1;
noGradient = false;
+ aamax = annotation.graphMax;
+ aamin = annotation.graphMin;
+ if (annotation.isRNA())
+ {
+ ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+ }
}
@Override
// resolve the context containing all the annotation for the sequence
AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
: alignment.getContext();
+ boolean f = true,rna=false;
for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
.getCalcId()))
{
&& (alan.label != null && annotation != null && alan.label
.equals(annotation.label)))
{
+ if (!rna && alan.isRNA())
+ {
+ rna = true;
+ }
seqannot.put(alan.sequenceRef, alan);
+ if (f || alan.graphMax > aamax)
+ {
+ aamax = alan.graphMax;
+ }
+ if (f || alan.graphMin < aamin)
+ {
+ aamin = alan.graphMin;
+ }
+ f = false;
}
}
+ if (rna)
+ {
+ ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+ }
}
}
+ float aamin = 0f, aamax = 0f;
public String getAnnotation()
{
return annotation.label;
}
else
{
- currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
- : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
- : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+ if (annotation.isRNA())
+ {
+ currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
+ }
+ else
+ {
+ currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
+ : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
+ : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+ }
}
}
else
}
else
{
- // calculate a shade
- float range = 1f;
- if (thresholdIsMinMax
- && annotation.threshold != null
- && aboveAnnotationThreshold == ABOVE_THRESHOLD
- && annotation.annotations[j].value >= annotation.threshold.value)
- {
- range = (annotation.annotations[j].value - annotation.threshold.value)
- / (annotation.graphMax - annotation.threshold.value);
- }
- else if (thresholdIsMinMax
- && annotation.threshold != null
- && aboveAnnotationThreshold == BELOW_THRESHOLD
- && annotation.annotations[j].value >= annotation.graphMin)
- {
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.threshold.value - annotation.graphMin);
- }
- else
- {
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.graphMax - annotation.graphMin);
- }
-
- int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
- * range + b1);
-
- currentColour = new Color(dr, dg, db);
-
+ currentColour = shadeCalculation(annotation, j);
}
}
if (conservationColouring)
return currentColour;
}
+ private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+ {
+
+ // calculate a shade
+ float range = 1f;
+ if (thresholdIsMinMax
+ && annotation.threshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && annotation.annotations[j].value >= annotation.threshold.value)
+ {
+ range = (annotation.annotations[j].value - annotation.threshold.value)
+ / (annotation.graphMax - annotation.threshold.value);
+ }
+ else if (thresholdIsMinMax && annotation.threshold != null
+ && aboveAnnotationThreshold == BELOW_THRESHOLD
+ && annotation.annotations[j].value >= annotation.graphMin)
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.threshold.value - annotation.graphMin);
+ }
+ else
+ {
+ if (annotation.graphMax != annotation.graphMin)
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.graphMax - annotation.graphMin);
+ }
+ else
+ {
+ range = 0f;
+ }
+ }
+
+ int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
+ * range + b1);
+
+ return new Color(dr, dg, db);
+
+ }
public boolean isPredefinedColours()
{
return predefinedColours;
return col;
}
+
+ public static Color rnaHelices[] = null;
+
+ public static void initRnaHelicesShading(int n)
+ {
+ int j = 0;
+ if (rnaHelices == null)
+ {
+ rnaHelices = new Color[n + 1];
+ }
+ else if (rnaHelices != null && rnaHelices.length <= n)
+ {
+ Color[] t = new Color[n + 1];
+ System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
+ j = rnaHelices.length;
+ rnaHelices = t;
+ }
+ else
+ {
+ return;
+ }
+ // Generate random colors and store
+ for (; j <= n; j++)
+ {
+ rnaHelices[j] = jalview.util.ColorUtils
+ .generateRandomColor(Color.white);
+ }
+ }
+
}
import jalview.analysis.scoremodels.PIDScoreModel;
import jalview.api.analysis.ScoreModelI;
-import java.util.*;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
import java.util.List;
-import java.awt.*;
+import java.util.Map;
+import java.util.Vector;
public class ResidueProperties
{
propMatrixF[i][j] = 0;
propMatrixPos[i][j] = 0;
propMatrixEpos[i][j] = 0;
- for (Enumeration<String> en = (Enumeration<String>) propHash.keys(); en
+ for (Enumeration<String> en = propHash.keys(); en
.hasMoreElements();)
{
String ph = en.nextElement();
* Used by getRNASecStrucState
*
*/
- public static Hashtable toRNAssState;
+ public static Hashtable<String, String> toRNAssState;
+
+ public static boolean RNAcloseParen[] = new boolean[255];
static
{
toRNAssState = new Hashtable<String, String>();
toRNAssState.put("y", "Y");
toRNAssState.put("Z", "Z");
toRNAssState.put("z", "Z");
-
+ for (int p = 0; p < RNAcloseParen.length; p++)
+ {
+ RNAcloseParen[p] = false;
+ }
+ for (String k : toRNAssState.keySet())
+ {
+ RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k)
+ .charAt(0);
+ }
}
/**
String ssc = ssstring.substring(i, i + 1);
if (toRNAssState.containsKey(ssc))
{
- ss.append((String) toRNAssState.get(ssc));
+ // valid ss character - so return it
+ ss.append(ssc); // (String) toRNAssState.get(ssc));
}
else
{
return ss.toString();
}
+ public static boolean isCloseParenRNA(char dc)
+ {
+ return RNAcloseParen[dc];
+ }
+
// main method generates perl representation of residue property hash
// / cut here
public static void main(String[] args)
System.out.println("};");
}
// to here
+
}
StructureMapping[] mappings;
+ private boolean processSecondaryStructure = false,
+ secStructServices = false, addTempFacAnnot = false;
+
+ /**
+ * @return true if will try to use external services for processing secondary
+ * structure
+ */
+ public boolean isSecStructServices()
+ {
+ return secStructServices;
+ }
+
+ /**
+ * control use of external services for processing secondary structure
+ *
+ * @param secStructServices
+ */
+ public void setSecStructServices(boolean secStructServices)
+ {
+ this.secStructServices = secStructServices;
+ }
+
+ /**
+ * flag controlling addition of any kind of structural annotation
+ *
+ * @return true if temperature factor annotation will be added
+ */
+ public boolean isAddTempFacAnnot()
+ {
+ return addTempFacAnnot;
+ }
+
+ /**
+ * set flag controlling addition of structural annotation
+ *
+ * @param addTempFacAnnot
+ */
+ public void setAddTempFacAnnot(boolean addTempFacAnnot)
+ {
+ this.addTempFacAnnot = addTempFacAnnot;
+ }
+
+ /**
+ *
+ * @return if true, the structure manager will attempt to add secondary
+ * structure lines for unannotated sequences
+ */
+
+ public boolean isProcessSecondaryStructure()
+ {
+ return processSecondaryStructure;
+ }
+
+ /**
+ * Control whether structure manager will try to annotate mapped sequences
+ * with secondary structure from PDB data.
+ *
+ * @param enable
+ */
+ public void setProcessSecondaryStructure(boolean enable)
+ {
+ processSecondaryStructure = enable;
+ }
+
/**
* debug function - write all mappings to stdout
*/
* the tried and tested MCview pdb mapping
*/
MCview.PDBfile pdb = null;
- boolean parseSecStr=true;
+ boolean parseSecStr = processSecondaryStructure;
if (isPDBFileRegistered(pdbFile))
{
for (SequenceI sq : sequence)
}
try
{
- pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol);
+ pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr,
+ secStructServices, pdbFile, protocol);
if (pdb.id != null && pdb.id.trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
{
package jalview.util;
import jalview.gui.EPSOptions;
+import jalview.gui.SVGOptions;
import jalview.io.JalviewFileChooser;
import java.awt.Component;
import javax.imageio.ImageIO;
import org.jfree.graphics2d.svg.SVGGraphics2D;
+import org.jfree.graphics2d.svg.SVGHints;
import org.jibble.epsgraphics.EpsGraphics2D;
public class ImageMaker
Graphics2D ig2 = (Graphics2D) graphics;
ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
+
}
void setupSVG(int width, int height, String title)
{
+
g2 = new SVGGraphics2D(width, height);
+ Graphics2D ig2 = g2;
+
+ String renderStyle = jalview.bin.Cache.getDefault("SVG_RENDERING",
+ "Prompt each time");
+
+ // If we need to prompt, and if the GUI is visible then
+ // Prompt for EPS rendering style
+ if (renderStyle.equalsIgnoreCase("Prompt each time")
+ && !(System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
+ {
+ SVGOptions svgOption = new SVGOptions();
+ renderStyle = svgOption.getValue();
+
+ if (renderStyle == null || svgOption.cancelled)
+ {
+ return;
+ }
+ }
+
+ if (renderStyle.equalsIgnoreCase("lineart"))
+ {
+ ig2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+ SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+ }
+
graphics = g2;
}
*/
package jalview.viewmodel;
-import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
AlignmentAnnotation alignmentAnnotation)
{
if (!alignmentAnnotation.autoCalculated)
+ {
return false;
+ }
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
// System.err.println("grey out ("+alignmentAnnotation.label+")");
selectionGroup = new SequenceGroup();
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- Vector tmp = alignment.getHiddenSequences().showAll(
+ List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
hiddenRepSequences);
- for (int t = 0; t < tmp.size(); t++)
+ for (SequenceI seq : tmp)
{
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ selectionGroup.addSequence(seq, false);
+ setSequenceAnnotationsVisible(seq, true);
}
hasHiddenRows = false;
public void showSequence(int index)
{
- Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
+ index,
hiddenRepSequences);
if (tmp.size() > 0)
{
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- for (int t = 0; t < tmp.size(); t++)
+ for (SequenceI seq : tmp)
{
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ selectionGroup.addSequence(seq, false);
+ setSequenceAnnotationsVisible(seq, true);
}
// JBPNote: refactor: only update flag if we modified visiblity (used to
// do this regardless)
for (int i = 0; i < seq.length; i++)
{
alignment.getHiddenSequences().hideSequence(seq[i]);
+ setSequenceAnnotationsVisible(seq[i], false);
}
hasHiddenRows = true;
firePropertyChange("alignment", null, alignment.getSequences());
}
}
+ /**
+ * Set visibility for any annotations for the given sequence.
+ *
+ * @param sequenceI
+ */
+ protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
+ boolean visible)
+ {
+ for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+ {
+ if (ann.sequenceRef == sequenceI)
+ {
+ ann.visible = visible;
+ }
+ }
+ }
+
public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
{
int sSize = sg.getSize();
*/
package jalview.ws.jws1;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.JobStateSummary;
import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.List;
+
import vamsas.objects.simple.JpredResult;
class JPredThread extends JWS1Thread implements WSClientI
sqs[i] = al.getSequenceAt(i);
}
if (!jalview.analysis.SeqsetUtils.deuniquify(
- (Hashtable) SequenceInfo, sqs))
+ SequenceInfo, sqs))
{
throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment")));
}
}
FirstSeq = 0;
- al.setDataset(null);
+ if (currentView.getDataset() != null)
+ {
+ al.setDataset(currentView.getDataset());
+ }
+ else
+ {
+ al.setDataset(null);
+ }
jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
FirstSeq, false, predMap);
if (predMap != null)
{
char gc = getGapChar();
- SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input
- .getAlignmentAndColumnSelection(gc))[0];
+ SequenceI[] sqs = (SequenceI[]) input
+ .getAlignmentAndColumnSelection(gc)[0];
if (this.msaIndex >= sqs.length)
{
throw new Error(MessageManager.getString("error.implementation_error_invalid_msa_index_for_job"));
}
else
{
- al.setDataset(null);
+ if (currentView.getDataset() != null)
+ {
+ al.setDataset(currentView.getDataset());
+
+ }
+ else
+ {
+ al.setDataset(null);
+ }
jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
FirstSeq, true, predMap);
SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
}
}
}
+ // transfer to dataset
+ for (AlignmentAnnotation alant : al.getAlignmentAnnotation())
+ {
+ if (alant.sequenceRef != null)
+ {
+ replaceAnnotationOnAlignmentWith(alant, alant.label,
+ "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"),
+ alant.sequenceRef);
+ }
+ }
return new Object[]
{ al, alcsel }; // , FirstSeq, noMsa};
}
/**
+ * copied from JabawsCalcWorker
+ *
+ * @param newAnnot
+ * @param typeName
+ * @param calcId
+ * @param aSeq
+ */
+ protected void replaceAnnotationOnAlignmentWith(
+ AlignmentAnnotation newAnnot, String typeName, String calcId,
+ SequenceI aSeq)
+ {
+ SequenceI dsseq = aSeq.getDatasetSequence();
+ while (dsseq.getDatasetSequence() != null)
+ {
+ dsseq = dsseq.getDatasetSequence();
+ }
+ // look for same annotation on dataset and lift this one over
+ List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(
+ calcId, typeName);
+ if (dsan != null && dsan.size() > 0)
+ {
+ for (AlignmentAnnotation dssan : dsan)
+ {
+ dsseq.removeAlignmentAnnotation(dssan);
+ }
+ }
+ AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
+ dsseq.addAlignmentAnnotation(dssan);
+ dssan.adjustForAlignment();
+ }
+
+ /**
* Given an alignment where all other sequences except profileseq are
* aligned to the ungapped profileseq, insert gaps in the other sequences to
* realign them with the residues in profileseq
{
if (job.getJobId().startsWith("Broken"))
{
- job.result = (vamsas.objects.simple.Result) new JpredResult();
+ job.result = new JpredResult();
job.result.setInvalid(true);
job.result.setStatus(MessageManager.formatMessage("label.submission_params", new String[]{job.getJobId().toString()}));
throw new Exception(job.getJobId());
{
continue;
}
+ String typename, calcName;
AlignmentAnnotation annot = createAnnotationRowsForScores(
ourAnnot,
- service.serviceType + " (" + scr.getMethod() + ")",
- service.getServiceTypeURI() + "/" + scr.getMethod(),
+ typename = service.serviceType + " ("
+ + scr.getMethod() + ")",
+ calcName = service.getServiceTypeURI() + "/"
+ + scr.getMethod(),
aseq, base + 1, scr);
annot.graph = AlignmentAnnotation.LINE_GRAPH;
}
}
annot._linecolour = col;
+ // finally, update any dataset annotation
+ replaceAnnotationOnAlignmentWith(annot, typename, calcName,
+ aseq);
}
}
}
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.util.HashSet;
import java.util.Set;
Jws2Discoverer jws2Discoverer = null;
- String jwsservers = null;
+ String jwsserver = null;
boolean quit = false, running = false;
this.quit = quit;
}
- public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String jwsservers)
+ public JabaWsServerQuery(Jws2Discoverer jws2Discoverer, String server)
{
this.jws2Discoverer = jws2Discoverer;
- this.jwsservers = jwsservers;
+ this.jwsserver = server;
}
Services[] JABAWS1SERVERS = new Services[]
running = true;
try
{
- if (Jws2Client.validURL(jwsservers))
+ // TODO this test doesn't seem to attempt a connection - should it?
+ // would save a lot of failed tries with UnknownHostException
+ if (isValidUrl(jwsserver))
{
compbio.data.msa.RegistryWS registry = null;
Set svccategories = null;
try
{
// JBPNote: why is RegistryWS in compbio.data.msa ?
- registry = Jws2Client.connectToRegistry(jwsservers);
+ registry = Jws2Client.connectToRegistry(jwsserver);
if (registry != null)
{
// System.err.println("Test Services Output\n"
ex.printStackTrace();
// if that failed, then we are probably working with a JABAWS1 server.
// in that case, look for each service endpoint
- System.err.println("JWS2 Discoverer: " + jwsservers
+ System.err.println("JWS2 Discoverer: " + jwsserver
+ " is a JABAWS1 server. Using hardwired list.");
for (Services srv : JABAWS1SERVERS)
{
JABAService service = null;
try
{
- service = Jws2Client.connect(jwsservers, srv);
+ service = Jws2Client.connect(jwsserver, srv);
} catch (Exception e)
{
System.err.println("Jws2 Discoverer: Problem on "
- + jwsservers + " with service " + srv + ":\n"
+ + jwsserver + " with service " + srv + ":\n"
+ e.getMessage());
if (!(e instanceof javax.xml.ws.WebServiceException))
{
e.printStackTrace();
}
// For moment, report service as a problem.
- jws2Discoverer.addInvalidServiceUrl(jwsservers);
+ jws2Discoverer.addInvalidServiceUrl(jwsserver);
}
;
if (service != null)
String description = registry.getServiceDescription(srv);
- svc = Jws2InstanceFactory.newJws2Instance(jwsservers,
+ svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
srv.toString(), cat.name, description, service);
}
if (svc == null)
{
- svc = Jws2InstanceFactory.newJws2Instance(jwsservers,
+ svc = Jws2InstanceFactory.newJws2Instance(jwsserver,
srv.toString(), cat.name,
"JABAWS 1 Alignment Service", service);
}
- jws2Discoverer.addService(jwsservers, svc);
+ jws2Discoverer.addService(jwsserver, svc);
}
}
if (noservices)
{
- jws2Discoverer.addUrlwithnoservices(jwsservers);
+ jws2Discoverer.addUrlwithnoservices(jwsserver);
}
}
else
{
- jws2Discoverer.addInvalidServiceUrl(jwsservers);
- Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
+ jws2Discoverer.addInvalidServiceUrl(jwsserver);
+ Cache.log.info("Ignoring invalid Jws2 service url " + jwsserver);
}
} catch (Exception e)
{
e.printStackTrace();
Cache.log.warn("Exception when discovering Jws2 services.", e);
- jws2Discoverer.addInvalidServiceUrl(jwsservers);
+ jws2Discoverer.addInvalidServiceUrl(jwsserver);
} catch (Error e)
{
Cache.log.error("Exception when discovering Jws2 services.", e);
- jws2Discoverer.addInvalidServiceUrl(jwsservers);
+ jws2Discoverer.addInvalidServiceUrl(jwsserver);
}
running = false;
}
+ /**
+ * Check if the URL is valid and responding.
+ *
+ * @return
+ */
+ private boolean isValidUrl(String server)
+ {
+ // return Jws2Client.validURL(jwsserver); // checks syntax only
+ boolean result = false;
+ if (server != null) {
+ try {
+ URL url = new URL(server);
+ url.openStream().close();
+ result = true;
+ } catch (MalformedURLException e)
+ {
+ System.err.println("Invalid server URL: " + server);
+ result = false;
+ } catch (IOException e)
+ {
+ System.err.println("Error connecting to server: " + server + ": "
+ + e.toString());
+ result = false;
+ }
+ }
+ return result;
+ }
+
}
return annotation;
}
+ protected void replaceAnnotationOnAlignmentWith(
+ AlignmentAnnotation newAnnot, String typeName, String calcId,
+ SequenceI aSeq)
+ {
+ SequenceI dsseq = aSeq.getDatasetSequence();
+ while (dsseq.getDatasetSequence() != null)
+ {
+ dsseq = dsseq.getDatasetSequence();
+ }
+ // look for same annotation on dataset and lift this one over
+ List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
+ typeName);
+ if (dsan != null && dsan.size() > 0)
+ {
+ for (AlignmentAnnotation dssan : dsan)
+ {
+ dsseq.removeAlignmentAnnotation(dssan);
+ }
+ }
+ AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
+ dsseq.addAlignmentAnnotation(dssan);
+ dssan.adjustForAlignment();
+ }
+
private void constructAnnotationFromScore(AlignmentAnnotation annotation,
int base, int alWidth, Score scr)
{
import java.awt.event.ActionListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
*/
public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
+
+ /*
+ * the .jalview_properties entry for JWS2 URLS
+ */
+ final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+
+ /*
+ * Singleton instance
+ */
+ private static Jws2Discoverer discoverer;
+
+ /*
+ * Override for testing only
+ */
+ private static List<String> testUrls = null;
+
+ // preferred url has precedence over others
+ private String preferredUrl;
+
+ private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
+ Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
+ validServiceUrls = null;
+
+ boolean running = false, aborted = false;
+
+ Thread oldthread = null;
+
+ /**
+ * holds list of services.
+ */
+ protected Vector<Jws2Instance> services;
+
+ /**
+ * Private constructor enforces use of singleton via getDiscoverer()
+ */
+ private Jws2Discoverer()
+ {
+ }
+
/**
* change listeners are notified of "services" property changes
*
changeSupport.removePropertyChangeListener(listener);
}
- boolean running = false, aborted = false;
-
/**
* @return the aborted
*/
public void setAborted(boolean aborted)
{
this.aborted = aborted;
- }
-
- Thread oldthread = null;
+ }
public void run()
{
// first set up exclusion list if needed
final Set<String> ignoredServices = new HashSet<String>();
- for (String ignored : jalview.bin.Cache.getDefault(
+ for (String ignored : Cache.getDefault(
"IGNORED_JABAWS_SERVICETYPES", "")
.split("\\|"))
{
ArrayList<String> svctypes = new ArrayList<String>();
List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
- for (final String jwsservers : getServiceUrls())
+ for (final String jwsserver : getServiceUrls())
{
- JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
+ JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
if (svctypes.size() == 0)
{
// TODO: remove this ugly hack to get Canonical JABA service ordering
Jws2Instance[] svcs = new Jws2Instance[services.size()];
int[] spos = new int[services.size()];
int ipos = 0;
- Vector svcUrls = getServiceUrls();
+ List<String> svcUrls = getServiceUrls();
for (Jws2Instance svc : services)
{
svcs[ipos] = svc;
}
/**
- * holds list of services.
- */
- protected Vector<Jws2Instance> services;
-
- /**
* attach all available web services to the appropriate submenu in the given
* JMenu
*/
{
if (args.length > 0)
{
- testUrls = new Vector<String>();
+ testUrls = new ArrayList<String>();
for (String url : args)
{
testUrls.add(url);
}
}
- private static Jws2Discoverer discoverer;
-
+ /**
+ * Returns the singleton instance of this class.
+ *
+ * @return
+ */
public static Jws2Discoverer getDiscoverer()
{
if (discoverer == null)
public boolean hasServices()
{
- // TODO Auto-generated method stub
return !running && services != null && services.size() > 0;
}
return running;
}
- /**
- * the jalview .properties entry for JWS2 URLS
- */
- final static String JWS2HOSTURLS = "JWS2HOSTURLS";
-
- public static void setServiceUrls(Vector<String> urls)
+ public void setServiceUrls(List<String> wsUrls)
{
- if (urls != null)
+ if (wsUrls != null && !wsUrls.isEmpty())
{
- StringBuffer urlbuffer = new StringBuffer();
+ StringBuilder urls = new StringBuilder(128);
String sep = "";
- for (String url : urls)
+ for (String url : wsUrls)
{
- urlbuffer.append(sep);
- urlbuffer.append(url);
+ urls.append(sep);
+ urls.append(url);
sep = ",";
}
- Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString());
+ Cache.setProperty(JWS2HOSTURLS, urls.toString());
}
else
{
}
}
- private static Vector<String> testUrls = null;
-
- public static Vector<String> getServiceUrls()
+ /**
+ * Returns web service URLs, in the order in which they should be tried (or an
+ * empty list).
+ *
+ * @return
+ */
+ public List<String> getServiceUrls()
{
if (testUrls != null)
{
// return test urls, if there are any, instead of touching cache
return testUrls;
}
- String surls = Cache.getDefault(JWS2HOSTURLS,
- "http://www.compbio.dundee.ac.uk/jabaws");
- Vector<String> urls = new Vector<String>();
+ List<String> urls = new ArrayList<String>();
+
+ if (this.preferredUrl != null)
+ {
+ urls.add(preferredUrl);
+ }
+
+ String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
try
{
StringTokenizer st = new StringTokenizer(surls, ",");
String url = null;
try
{
- java.net.URL u = new java.net.URL(url = st.nextToken());
+ url = st.nextToken();
+ new URL(url);
if (!urls.contains(url))
{
urls.add(url);
}
else
{
- jalview.bin.Cache.log.info("Ignoring duplicate url in "
+ Cache.log.info("Ignoring duplicate url " + url + " in "
+ JWS2HOSTURLS + " list");
}
- } catch (Exception ex)
+ } catch (MalformedURLException ex)
{
- jalview.bin.Cache.log
+ Cache.log
.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- jalview.bin.Cache.log
+ Cache.log
.warn("This was probably due to a malformed comma separated list"
+ " in the "
+ JWS2HOSTURLS
+ " entry of $(HOME)/.jalview_properties)");
- jalview.bin.Cache.log.debug("Exception was ", ex);
+ Cache.log.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log.warn(
+ Cache.log.warn(
"Error parsing comma separated list of urls in "
+ JWS2HOSTURLS + " preference.", ex);
}
- if (urls.size() >= 0)
- {
- return urls;
- }
- return null;
+ return urls;
}
public Vector<Jws2Instance> getServices()
return thr;
}
- Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
- validServiceUrls = null;
-
/**
* @return the invalidServiceUrls
*/
return 1;
}
if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
+ {
return 0;
+ }
if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
{
return -1;
{
setPreferredServiceFor(null, serviceType, serviceAction, selectedServer);
}
+
+ /**
+ * Set a URL to try before any others. For use with command-line parameter to
+ * configure a local Jabaws installation without the need to add to property
+ * files.
+ *
+ * @param value
+ * @throws MalformedURLException
+ */
+ public void setPreferredUrl(String value) throws MalformedURLException
+ {
+ if (value != null && value.trim().length() > 0)
+ {
+ new URL(value);
+ preferredUrl = value;
+ }
+ }
}
*/
package jalview.ws.jws2;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.WsParamSetI;
+
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
import java.util.List;
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.ToolTipManager;
-import jalview.datamodel.*;
-import jalview.gui.*;
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.WsParamSetI;
/**
* DOCUMENT ME!
if (!(sh.service instanceof MsaWS))
{
// redundant at mo - but may change
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager.formatMessage("label.service_called_is_not_msa_service", new String[]{sh.serviceType}),
- MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.service_called_is_not_msa_service",
+ new String[]
+ { sh.serviceType }), MessageManager
+ .getString("label.internal_jalview_error"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
server = (MsaWS) sh.service;
if ((wsInfo = setWebService(sh, false)) == null)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.msa_service_is_unknown", new String[]{sh.serviceType}),
- MessageManager.getString("label.internal_jalview_error"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.msa_service_is_unknown", new String[]
+ { sh.serviceType }), MessageManager
+ .getString("label.internal_jalview_error"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
"label.run_with_preset_params", new String[]
{ calcName }));
+ final int showToolTipFor = ToolTipManager.sharedInstance()
+ .getDismissDelay();
for (final WsParamSetI preset : presets)
{
final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<p><strong>"
- + (preset.isModifiable() ? MessageManager.getString("label.user_preset")
- : MessageManager.getString("label.service_preset")) + "</strong><br/>"
- + preset.getDescription() + "</p>"));
+ final int QUICK_TOOLTIP = 1500;
+ // JAL-1582 shorten tooltip display time in these menu items as
+ // they can obscure other options
+ methodR.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ ToolTipManager.sharedInstance().setDismissDelay(
+ QUICK_TOOLTIP);
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
+ }
+
+ });
+ methodR.setToolTipText(JvSwingUtils.wrapTooltip(
+ true,
+ "<p><strong>"
+ + (preset.isModifiable() ? MessageManager
+ .getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preset.getDescription()
+ + "</p>"));
methodR.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
--- /dev/null
+package jalview.commands;
+
+import static org.junit.Assert.assertEquals;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+
+/**
+ * Unit tests for EditCommand
+ *
+ * @author gmcarstairs
+ *
+ */
+public class EditCommandTest
+{
+
+ private EditCommand testee;
+
+ private SequenceI[] seqs;
+
+ private Alignment al;
+
+ @Before
+ public void setUp()
+ {
+ testee = new EditCommand();
+ seqs = new SequenceI[4];
+ seqs[0] = new Sequence("seq0", "abcdefghjk");
+ seqs[1] = new Sequence("seq1", "fghjklmnopq");
+ seqs[2] = new Sequence("seq2", "qrstuvwxyz");
+ seqs[3] = new Sequence("seq3", "1234567890");
+ al = new Alignment(seqs);
+ al.setGapCharacter('?');
+ }
+
+ /**
+ * Test inserting gap characters
+ */
+ @Test
+ public void testAppendEdit_insertGap()
+ {
+ // set a non-standard gap character to prove it is actually used
+ testee.appendEdit(Action.INSERT_GAP, seqs, 4, 3, al, true);
+ assertEquals("abcd???efghjk", seqs[0].getSequenceAsString());
+ assertEquals("fghj???klmnopq", seqs[1].getSequenceAsString());
+ assertEquals("qrst???uvwxyz", seqs[2].getSequenceAsString());
+ assertEquals("1234???567890", seqs[3].getSequenceAsString());
+
+ // todo: test for handling out of range positions?
+ }
+
+ /**
+ * Test deleting characters from sequences. Note the deleteGap() action does
+ * not check that only gap characters are being removed.
+ */
+ @Test
+ public void testAppendEdit_deleteGap()
+ {
+ testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true);
+ assertEquals("abcdhjk", seqs[0].getSequenceAsString());
+ assertEquals("fghjnopq", seqs[1].getSequenceAsString());
+ assertEquals("qrstxyz", seqs[2].getSequenceAsString());
+ assertEquals("1234890", seqs[3].getSequenceAsString());
+ }
+
+ /**
+ * Test a cut action. The command should store the cut characters to support
+ * undo.
+ */
+ @Test
+ public void testCut()
+ {
+ Edit ec = testee.new Edit(Action.CUT, seqs, 4, 3, al);
+ testee.cut(ec, new AlignmentI[]
+ { al });
+ assertEquals("abcdhjk", seqs[0].getSequenceAsString());
+ assertEquals("fghjnopq", seqs[1].getSequenceAsString());
+ assertEquals("qrstxyz", seqs[2].getSequenceAsString());
+ assertEquals("1234890", seqs[3].getSequenceAsString());
+
+ assertEquals("efg", new String(ec.string[0]));
+ assertEquals("klm", new String(ec.string[1]));
+ assertEquals("uvw", new String(ec.string[2]));
+ assertEquals("567", new String(ec.string[3]));
+ // TODO: case where whole sequence is deleted as nothing left; etc
+ }
+
+ /**
+ * Test a Paste action, where this adds sequences to an alignment.
+ */
+ @Test
+ @Ignore
+ // TODO fix so it works
+ public void testPaste_addToAlignment()
+ {
+ SequenceI[] newSeqs = new SequenceI[2];
+ newSeqs[0] = new Sequence("newseq0", "ACEFKL");
+ newSeqs[1] = new Sequence("newseq1", "JWMPDH");
+
+ Edit ec = testee.new Edit(Action.PASTE, newSeqs, 0, al.getWidth(), al);
+ testee.paste(ec, new AlignmentI[]
+ { al });
+ assertEquals(6, al.getSequences().size());
+ assertEquals("1234567890", seqs[3].getSequenceAsString());
+ assertEquals("ACEFKL", seqs[4].getSequenceAsString());
+ assertEquals("JWMPDH", seqs[5].getSequenceAsString());
+ }
+
+ /**
+ * Test insertGap followed by undo command
+ */
+ @Test
+ public void testUndo_insertGap()
+ {
+ // Edit ec = testee.new Edit(Action.INSERT_GAP, seqs, 4, 3, '?');
+ testee.appendEdit(Action.INSERT_GAP, seqs, 4, 3, al, true);
+ // check something changed
+ assertEquals("abcd???efghjk", seqs[0].getSequenceAsString());
+ testee.undoCommand(new AlignmentI[]
+ { al });
+ assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
+ assertEquals("fghjklmnopq", seqs[1].getSequenceAsString());
+ assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
+ assertEquals("1234567890", seqs[3].getSequenceAsString());
+ }
+
+ /**
+ * Test deleteGap followed by undo command
+ */
+ @Test
+ public void testUndo_deleteGap()
+ {
+ testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true);
+ // check something changed
+ assertEquals("abcdhjk", seqs[0].getSequenceAsString());
+ testee.undoCommand(new AlignmentI[]
+ { al });
+ // deleteGap doesn't 'remember' deleted characters, only gaps get put back
+ assertEquals("abcd???hjk", seqs[0].getSequenceAsString());
+ assertEquals("fghj???nopq", seqs[1].getSequenceAsString());
+ assertEquals("qrst???xyz", seqs[2].getSequenceAsString());
+ assertEquals("1234???890", seqs[3].getSequenceAsString());
+ }
+
+ /**
+ * Test several commands followed by an undo command
+ */
+ @Test
+ public void testUndo_multipleCommands()
+ {
+ // delete positions 3/4/5 (counting from 1)
+ testee.appendEdit(Action.DELETE_GAP, seqs, 2, 3, al, true);
+ assertEquals("abfghjk", seqs[0].getSequenceAsString());
+ assertEquals("1267890", seqs[3].getSequenceAsString());
+
+ // insert 2 gaps after the second residue
+ testee.appendEdit(Action.INSERT_GAP, seqs, 2, 2, al, true);
+ assertEquals("ab??fghjk", seqs[0].getSequenceAsString());
+ assertEquals("12??67890", seqs[3].getSequenceAsString());
+
+ // delete positions 4/5/6
+ testee.appendEdit(Action.DELETE_GAP, seqs, 3, 3, al, true);
+ assertEquals("ab?hjk", seqs[0].getSequenceAsString());
+ assertEquals("12?890", seqs[3].getSequenceAsString());
+
+ // undo edit commands
+ testee.undoCommand(new AlignmentI[]
+ { al });
+ assertEquals("ab?????hjk", seqs[0].getSequenceAsString());
+ assertEquals("12?????890", seqs[3].getSequenceAsString());
+ }
+
+ /**
+ * Unit test for JAL-1594 bug: click and drag sequence right to insert gaps -
+ * undo did not remove them all.
+ */
+ @Test
+ public void testUndo_multipleInsertGaps()
+ {
+ testee.appendEdit(Action.INSERT_GAP, seqs, 4, 1, al, true);
+ testee.appendEdit(Action.INSERT_GAP, seqs, 5, 1, al, true);
+ testee.appendEdit(Action.INSERT_GAP, seqs, 6, 1, al, true);
+
+ // undo edit commands
+ testee.undoCommand(new AlignmentI[]
+ { al });
+ assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
+ assertEquals("1234567890", seqs[3].getSequenceAsString());
+
+ }
+
+ /**
+ * Test cut followed by undo command
+ */
+ @Test
+ public void testUndo_cut()
+ {
+ testee.appendEdit(Action.CUT, seqs, 4, 3, al, true);
+ // check something changed
+ assertEquals("abcdhjk", seqs[0].getSequenceAsString());
+ testee.undoCommand(new AlignmentI[]
+ { al });
+ assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
+ assertEquals("fghjklmnopq", seqs[1].getSequenceAsString());
+ assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
+ assertEquals("1234567890", seqs[3].getSequenceAsString());
+ }
+
+ /**
+ * Test the replace command (used to manually edit a sequence)
+ */
+ @Test
+ public void testReplace()
+ {
+ // seem to need a dataset sequence on the edited sequence here
+ seqs[1].setDatasetSequence(seqs[1]);
+ new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[]
+ { seqs[1] }, 4, 8, al);
+ assertEquals("abcdefghjk", seqs[0].getSequenceAsString());
+ assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString());
+ assertEquals("1234567890", seqs[3].getSequenceAsString());
+ seqs[1] = new Sequence("seq1", "fghjZXYnopq");
+
+ }
+}
{
for (String pdbStr : testFile)
{
- PDBfile mctest = new PDBfile(false, false, pdbStr,
+ PDBfile mctest = new PDBfile(false, false, false, pdbStr,
AppletFormatAdapter.FILE);
PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
jalview.io.AppletFormatAdapter.FILE);
package jalview.ext.paradise;
import static org.junit.Assert.assertTrue;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
-import jalview.ext.paradise.Annotate3D;
import jalview.io.FastaFile;
import jalview.io.FormatAdapter;
iline = id.readLine();
fline = file.readLine();
if (iline != null)
+ {
System.out.println(iline);
+ }
if (fline != null)
+ {
System.out.println(fline);
+ }
// next assert fails for latest RNAview - because the XMLID entries
// change between file and ID based RNAML generation.
assertTrue(
@Test
public void testPDBfileVsRNAML() throws Exception
{
- PDBfile pdbf = new PDBfile(true,true,"examples/2GIS.pdb", FormatAdapter.FILE);
+ PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
+ FormatAdapter.FILE);
Assert.assertTrue(pdbf.isValid());
// Comment - should add new FileParse constructor like new FileParse(Reader
// ..). for direct reading
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.assertTrue;
+import jalview.gui.Help.HelpId;
+
+import java.net.URL;
+
+import javax.help.HelpSet;
+import javax.help.HelpSetException;
+import javax.help.Map;
+
+import org.junit.Test;
+
+public class HelpTest
+{
+ @Test
+ public void checkHelpTargets() throws HelpSetException
+ {
+ ClassLoader cl = Desktop.class.getClassLoader();
+ URL url = HelpSet.findHelpSet(cl, "help/help"); // $NON-NLS-$
+ HelpSet hs = new HelpSet(cl, url);
+ Map targets = hs.getLocalMap();
+
+ for (HelpId id : HelpId.values())
+ {
+ String target = id.toString();
+ assertTrue("Unmatched target enum: " + target,
+ targets.isValidID(target, hs));
+ }
+
+ }
+}
*/
package jalview.io;
-import static org.junit.Assert.*;
-
import java.io.File;
import org.junit.AfterClass;
public void testRnamlToStockholmIO()
{
StockholmFileTest.testFileIOwithFormat(new File(
- "examples/rna-alignment.xml"), "STH");
+ "examples/rna-alignment.xml"), "STH", -1, -1);
}
*/
package jalview.io;
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import jalview.datamodel.Alignment;
@Test
public void pfamFileIO() throws Exception
{
- testFileIOwithFormat(new File(PfamFile), "STH");
+ testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
}
@Test
@Test
public void rfamFileIO() throws Exception
{
- testFileIOwithFormat(new File(RfamFile), "STH");
+ testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
}
/**
* - label for IO class used to write and read back in the data from
* f
*/
- public static void testFileIOwithFormat(File f, String ioformat)
+ public static void testFileIOwithFormat(File f, String ioformat,
+ int naliannot, int nminseqann)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
+ ioformat + "' writer",
ioformat.equals(identifyoutput));
testAlignmentEquivalence(al, al_input);
+ int numaliannot = 0, numsqswithali = 0;
+ for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
+ {
+ if (ala.sequenceRef == null)
+ {
+ numaliannot++;
+ }
+ else
+ {
+ numsqswithali++;
+ }
+ }
+ if (naliannot > -1)
+ {
+ assertEquals("Number of alignment annotations", naliannot,
+ numaliannot);
+ }
+
+ assertTrue(
+ "Number of sequence associated annotations wasn't at least "
+ + nminseqann, numsqswithali >= nminseqann);
+
} catch (Exception e)
{
e.printStackTrace();
*/
package jalview.ws.jabaws;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
import jalview.ws.jws2.Jws2Discoverer;
import java.util.Vector;
services.add(url);
}
;
- Jws2Discoverer.setServiceUrls(services);
+ Jws2Discoverer.getDiscoverer().setServiceUrls(services);
}
try
{
git://source.jalview.org / jalview.git / commitdiff