jalview.release=releases/Release_2_10_4_Branch
-jalview.version=2.10.4
+jalview.version=2.10.4b1
jalview.ext.android includes code taken from the Android Open Source Project (https://android.googlesource.com/platform/frameworks/base/+/master/core/java/android/util).
The Apache 2.0 Licence (http://www.apache.org/licenses/LICENSE-2.0) is acknowledged in the source code.
+ org.stackoverflowusers.file.WindowsShortcuts was downloaded from http://github.com/codebling/WindowsShortcuts via https://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java
Licensing information for each library is given below:
</target>
<target name="buildindices" depends="init, prepare" unless="help.uptodate">
+ <replace value="${JALVIEW_VERSION}">
+ <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
+ <fileset dir="${outputDir}/${helpDir}">
+ <include name="help.jhm" />
+ </fileset>
+ </replace>
+
<java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
<arg line="html" />
</java>
CLUSTAL
-FER_CAPAA/1-97 -----------------------------------------------------------A
-FER_CAPAN/1-144 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA
-FER1_SOLLC/1-144 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA
-Q93XJ9_SOLTU/1-144 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA
-FER1_PEA/1-149 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA
-Q7XA98_TRIPR/1-152 MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMA
-FER1_MESCR/1-148 MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMA
-FER1_SPIOL/1-147 MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMA
-FER3_RAPSA/1-96 -----------------------------------------------------------A
-FER1_ARATH/1-148 MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMA
-FER_BRANA/1-96 -----------------------------------------------------------A
-FER2_ARATH/1-148 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA
-Q93Z60_ARATH/1-118 MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMA
-FER1_MAIZE/1-150 MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQA
-O80429_MAIZE/1-140 MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQA
-1A70|/1-97 -----------------------------------------------------------A
-
-FER_CAPAA/1-97 SYKVKLITPDGPIEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG
-FER_CAPAN/1-144 SYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDG
-FER1_SOLLC/1-144 SYKVKLITPEGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDG
-Q93XJ9_SOLTU/1-144 SYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDG
-FER1_PEA/1-149 SYKVKLVTPDGTQEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDG
-Q7XA98_TRIPR/1-152 TYKVKLITPEGPQEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDG
-FER1_MESCR/1-148 AYKVTLVTPEGKQELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDG
-FER1_SPIOL/1-147 AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ
-FER3_RAPSA/1-96 TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
-FER1_ARATH/1-148 TYKVKFITPEGELEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
-FER_BRANA/1-96 TYKVKFITPEGEQEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDE
-FER2_ARATH/1-148 TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ
-Q93Z60_ARATH/1-118 TYKVKFITPEGEQEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQ
-FER1_MAIZE/1-150 TYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQ
-O80429_MAIZE/1-140 TYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQ
-1A70|/1-97 AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQ
-
-FER_CAPAA/1-97 NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
-FER_CAPAN/1-144 NFLDDDQLEEGWVLTCVAYPQSDVTIETHKEAELVG-
-FER1_SOLLC/1-144 NFLDEDQEAAGFVLTCVAYPKGDVTIETHKEEELTA-
-Q93XJ9_SOLTU/1-144 KFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTA-
-FER1_PEA/1-149 SFLDDEQIEAGFVLTCVAYPTSDVVIETHKEEDLTA-
-Q7XA98_TRIPR/1-152 SFLDDEQIEGGWVLTCVAFPTSDVTIETHKEEELTA-
-FER1_MESCR/1-148 SFLDDDQIKEGWVLTCVAYPTGDVTIETHKEEELTA-
-FER1_SPIOL/1-147 SFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA-
-FER3_RAPSA/1-96 SFLDDDQIAEGFVLTCAAYPTSDVTIETHREEDMV--
-FER1_ARATH/1-148 SFLDDEQIGEGFVLTCAAYPTSDVTIETHKEEDIV--
-FER_BRANA/1-96 SFLDDDQIAEGFVLTCAAYPTSDVTIETHKEEELV--
-FER2_ARATH/1-148 SFLDDEQMSEGYVLTCVAYPTSDVVIETHKEEAIM--
-Q93Z60_ARATH/1-118 SFLDD--------------------------------
-FER1_MAIZE/1-150 SYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA
-O80429_MAIZE/1-140 SFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL--
-1A70|/1-97 SFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA
-
+FER_CAPAA/1-97 -----------------------------------------------------------A 1
+FER_CAPAN/1-144 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA 48
+FER1_SOLLC/1-144 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48
+Q93XJ9_SOLTU/1-144 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48
+FER1_PEA/1-149 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA 53
+
+FER_CAPAA/1-97 SYKVKLI 8
+FER_CAPAN/1-144 SYKVKLI 55
+FER1_SOLLC/1-144 SYKVKLI 55
+Q93XJ9_SOLTU/1-144 SYKVKLI 55
+FER1_PEA/1-149 SYKVKLV 60
<mapID target="home" url="html/index.html" />
<mapID target="new" url="html/whatsNew.html"/>
- <mapID target="release" url="html/releases.html#Jalview.2.10.4"/>
+ <mapID target="release" url="html/releases.html#Jalview.$$Version-Rel$$"/>
<mapID target="alannotation" url="html/features/annotation.html"/>
<mapID target="keys" url="html/keys.html"/>
<mapID target="newkeys" url="html/features/newkeystrokes.html"/>
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>8/05/2018</em></strong>
+ <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
+ <em>27/05/2018</em></strong>
+ </div>
+ </td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-1460 -->Windows File Shortcuts can be dragged
+ onto the Jalview Desktop
+ </li>
+ </ul>
+ </div></td>
+ <td><div align="left">
+ <em></em>
+ <ul>
+ <li>
+ <!-- JAL-2997 -->Clustal files with sequence positions in
+ right-hand column parsed correctly
+ </li>
+ <li>
+ <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
+ window has input focus
+ </li>
+ <li>
+ <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
+ not alignment area in exported graphic
+ </li>
+ <li>
+ <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
+ Jalview desktop on Windows doesn't open file<br />
+ <em>Dragging the currently open URL and links from a page viewed in Firefox or Chrome on
+ Windows is now fully supported. If you are using Edge, only
+ links in the page can be dragged, and with Internet Explorer, only
+ the currently open URL in the browser can be dropped onto
+ Jalview.</em>
+ </li>
+ <li>
+ <!-- JAL-2992 -->
+ </li>
+ </ul>
+ </div></td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
</div>
</td>
<td><div align="left">
overlapping alignment panel
</li>
<li>
- <!-- JAL-2929 -->overview doesn't show end of unpadded
+ <!-- JAL-2929 -->Overview doesn't show end of unpadded
sequence as gaps
</li>
<li>
- <!-- JAL-2789, JAL-2893 -->Cross-reference handling improved: CDS not handled correctly if transcript has no UTR
+ <!-- JAL-2789, JAL-2893 -->Cross-reference handling
+ improved: CDS not handled correctly if transcript has no
+ UTR
</li>
<li>
-
+ <!-- JAL-2321 -->Secondary structure and temperature
+ factor annotation not added to sequence when local PDB
+ file associated with it by drag'n'drop or structure
+ chooser
+ </li>
+ <li>
+ <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
+ dialog doesn't import PDB files dropped on an alignment
</li>
<li>
<!-- JAL-2666 -->Linked scrolling via protein horizontal
columns in annotation row
</li>
<li>
- <!-- JAL-2913 -->Preferences panel's ID Width control is
- honored in interactive and batch mode
+ <!-- JAL-2913 -->Preferences panel's ID Width control is not
+ honored in batch mode
</li>
<li>
<!-- JAL-2945 -->Linked sequence highlighting doesn't work
as generated by CONSURF)
</li>
<li>
+ <!-- JAL-2920 -->Uniprot 'sequence variant' features
+ tooltip doesn't include a text description of mutation
+ </li>
+ <li>
<!-- JAL-2922 -->Invert displayed features very slow when
structure and/or overview windows are also shown
</li>
label.autoadd_secstr = Add secondary structure annotation to alignment
label.autoadd_temp = Add Temperature Factor annotation to alignment
label.structure_viewer = Default structure viewer
+label.double_click_to_browse = Double-click to browse for file
label.chimera_path = Path to Chimera program
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.groups = All groups
label.selected_group = Selected group
label.use_info_for_height = Use Information Content as Letter Height
+action.search = Search
\ No newline at end of file
action.export_features=Exportar CaracterÃsticas
error.invalid_regex=Expresión regular inválida
label.autoadd_temp=Añadir anotación factor de temperatura al alineamiento
+label.double_click_to_browse = Haga doble clic para buscar fichero
label.chimera_path_tip=Jalview intentará primero las rutas introducidas aquÃ, Y si no las rutas usuales de instalación
label.structure_chooser=Selector de Estructuras
label.structure_chooser_manual_association=Selector de Estructuras - asociación manual
label.aacon_calculations=cálculos AACon
label.pdb_web-service_error=Error de servicio web PDB
exception.unable_to_detect_internet_connection=Jalview no puede detectar una conexión a Internet
-label.chimera_path=Ruta de acceso a programa Chimera
+label.chimera_path=Ruta de acceso a Chimera
warn.delete_all=<html>Borrar todas las secuencias cerrará la ventana del alineamiento.<br>Confirmar o Cancelar.
label.select_all=Seleccionar Todos
label.alpha_helix=Hélice Alfa
label.chimera_help=Ayuda para Chimera
label.find_tip=Buscar alineamiento, selección o IDs de secuencia para una subsecuencia (sin huecos)
-label.structure_viewer=Visualizador de estructura por defecto
+label.structure_viewer=Visualizador por defecto
label.embbed_biojson=Incrustar BioJSON al exportar HTML
label.transparency_tip=Ajustar la transparencia a "ver a través" los colores de las caracterÃsticas.
label.choose_annotations=Escoja anotaciones
label.most_polymer_residues = Más Residuos de PolÃmeros
label.cached_structures = Estructuras en Caché
label.free_text_search = Búsqueda de texto libre
+action.search = Buscar
\ No newline at end of file
</field>
<field name="position">
<bind-xml name="position" node="attribute" location="location/position"/>
- </field>
+ </field>
<field name="begin">
<bind-xml name="position" node="attribute" location="location/begin"/>
- </field>
- <field name="end">
- <bind-xml name="position" node="attribute" location="location/end"/>
- </field>
+ </field>
+ <field name="end">
+ <bind-xml name="position" node="attribute" location="location/end"/>
+ </field>
+ <field name="variation">
+ <bind-xml name="variation"/>
+ </field>
+ <field name="original">
+ <bind-xml name="original"/>
+ </field>
</class>
<class name="jalview.datamodel.xdb.uniprot.UniprotSequence">
import jalview.bin.Cache;
import jalview.gui.Preferences;
+import jalview.util.FileUtils;
import java.io.File;
import java.io.IOException;
this.haveGUI = haveGUI;
// Create the Chimera interface
chimeraManager = new ChimeraManager(this);
- chimSelectionList = new ArrayList<ChimeraStructuralObject>();
+ chimSelectionList = new ArrayList<>();
pathProps = new Properties();
}
ModelType type)
{
// new models
- Map<String, List<ChimeraModel>> newModels = new HashMap<String, List<ChimeraModel>>();
+ Map<String, List<ChimeraModel>> newModels = new HashMap<>();
if (chimObjNames.size() > 0)
{
List<String> names = chimObjNames.iterator().next();
// alDialog.dispose();
// }
// System.out.println("launch align dialog");
- List<ChimeraStructuralObject> chimObjectList = new ArrayList<ChimeraStructuralObject>();
+ List<ChimeraStructuralObject> chimObjectList = new ArrayList<>();
for (ChimeraModel model : chimeraManager.getChimeraModels())
{
if (useChains)
public List<String> getAllChimeraResidueAttributes()
{
- List<String> attributes = new ArrayList<String>();
+ List<String> attributes = new ArrayList<>();
// attributes.addAll(rinManager.getResAttrs());
attributes.addAll(chimeraManager.getAttrList());
return attributes;
// TODO: [Optional] Change priority of Chimera paths
public static List<String> getChimeraPaths()
{
- List<String> pathList = new ArrayList<String>();
+ List<String> pathList = new ArrayList<>();
// if no network is available and the settings have been modified by the
// user, check for a
}
else if (os.startsWith("Windows"))
{
- pathList.add("\\Program Files\\Chimera\\bin\\chimera");
- pathList.add("C:\\Program Files\\Chimera\\bin\\chimera.exe");
+ /*
+ * typical Windows installation path is
+ * C:\Program Files\Chimera 1.12\bin\chimera.exe
+ */
+ // current drive:
+ pathList.addAll(FileUtils.findMatches("\\",
+ "Program Files*/Chimera*/bin/{chimera,chimera.exe}"));
+ // C: drive (note may add as duplicates)
+ pathList.addAll(FileUtils.findMatches("C:\\",
+ "Program Files*/Chimera*/bin/{chimera,chimera.exe}"));
}
else if (os.startsWith("Mac"))
{
import java.util.Map;
import java.util.Vector;
+import javax.swing.LookAndFeel;
import javax.swing.UIManager;
import groovy.lang.Binding;
}
if (Platform.isAMac())
{
+
+ LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
+ .getLookAndFeel();
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
"Jalview");
System.setProperty("apple.laf.useScreenMenuBar", "true");
- try
- {
- UIManager.setLookAndFeel(
- ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel());
- } catch (Throwable e)
+ if (lookAndFeel != null)
{
- System.err.println(
- "Failed to set QuaQua look and feel: " + e.toString());
+ try
+ {
+ UIManager.setLookAndFeel(lookAndFeel);
+ } catch (Throwable e)
+ {
+ System.err.println(
+ "Failed to set QuaQua look and feel: " + e.toString());
+ }
}
- if (!ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel()
- .equals(UIManager.getLookAndFeel()))
+ if (lookAndFeel == null || !(lookAndFeel.getClass()
+ .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
+ || !UIManager.getLookAndFeel().getClass().toString()
+ .toLowerCase().contains("quaqua"))
{
try
{
System.err.println(
- "Quaqua LaF not available. Using VAqua(4).");
- // UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
+ "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
+ UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
} catch (Throwable e)
{
System.err.println(
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel;
public final class HiddenCursorPosition
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel;
import java.util.Iterator;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel;
import java.util.ArrayList;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel;
import java.util.ArrayList;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel;
import java.util.ArrayList;
{
private String type;
- private String description;
+ private String description = null;
+
+ private String original = null;
+
+ private String variation = null;
private String status;
public String getDescription()
{
- return description;
+ if (description == null && variation == null && original == null)
+ {
+ return null;
+ }
+ return (description == null ? "" : description)
+ + (variation != null
+ ? (description != null ? " " : "") + "Variation: '"
+ + variation + "'"
+ : "")
+ + (original != null
+ ? ((description != null || variation != null) ? " "
+ : "") + "Original: '" + original + "'"
+ : "");
}
public void setDescription(String d)
this.begin = p;
this.end = p;
}
+
+ public String getOriginal()
+ {
+ return original;
+ }
+
+ public void setOriginal(String original)
+ {
+ this.original = original;
+ }
+
+ public String getVariation()
+ {
+ return variation;
+ }
+
+ public void setVariation(String variant)
+ {
+ this.variation = variant;
+ }
}
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureImportSettings;
import jalview.util.Format;
import jalview.util.MessageManager;
{
Viewer viewer = null;
+ public JmolParser(boolean immediate, String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ super(immediate, inFile, sourceType);
+ }
+
public JmolParser(String inFile, DataSourceType sourceType)
throws IOException
{
}
lastID = tmpatom.resNumIns.trim();
}
- xferSettings();
+ if (isParseImmediately())
+ {
+ // configure parsing settings from the static singleton
+ xferSettings();
+ }
makeResidueList();
makeCaBondList();
prot.add(chainseq);
}
- if (StructureImportSettings.isProcessSecondaryStructure())
+ // look at local setting for adding secondary tructure
+ if (predictSecondaryStructure)
{
createAnnotation(chainseq, chain, ms.at);
}
alignPanel.setOverviewPanel(null);
};
});
+ if (getKeyListeners().length > 0)
+ {
+ frame.addKeyListener(getKeyListeners()[0]);
+ }
alignPanel.setOverviewPanel(overview);
}
int assocfiles = 0;
if (filesmatched.size() > 0)
{
- if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
- || JvOptionPane.showConfirmDialog(thisaf,
- MessageManager.formatMessage(
- "label.automatically_associate_structure_files_with_sequences_same_name",
- new Object[]
- { Integer.valueOf(filesmatched.size())
- .toString() }),
- MessageManager.getString(
- "label.automatically_associate_structure_files_by_name"),
- JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
-
+ boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+ if (!autoAssociate)
+ {
+ String msg = MessageManager.formatMessage(
+ "label.automatically_associate_structure_files_with_sequences_same_name",
+ new Object[]
+ { Integer.valueOf(filesmatched.size())
+ .toString() });
+ String ttl = MessageManager.getString(
+ "label.automatically_associate_structure_files_by_name");
+ int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
+ ttl, JvOptionPane.YES_NO_OPTION);
+ autoAssociate = choice == JvOptionPane.YES_OPTION;
+ }
+ if (autoAssociate)
{
for (Object[] fm : filesmatched)
{
alignPanel.paintAlignment(true, false);
}
}
+ else
+ {
+ /*
+ * add declined structures as sequences
+ */
+ for (Object[] o : filesmatched)
+ {
+ filesnotmatched.add((String) o[0]);
+ }
+ }
}
if (filesnotmatched.size() > 0)
{
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics;
-import java.awt.Insets;
import java.awt.event.AdjustmentEvent;
import java.awt.event.AdjustmentListener;
import java.awt.event.ComponentAdapter;
/*
* Estimate available height in the AlignFrame for alignment +
* annotations. Deduct an estimate for title bar, menu bar, scale panel,
- * hscroll, status bar (as these are not laid out we can't inspect their
- * actual heights). Insets gives frame borders.
+ * hscroll, status bar, insets.
*/
- int stuff = Platform.isAMac() ? 80 : 100;
- Insets insets = alignFrame.getInsets();
- int availableHeight = alignFrame.getHeight() - stuff - insets.top
- - insets.bottom;
+ int stuff = Platform.isAMac() ? 120 : 140;
+ int availableHeight = alignFrame.getHeight() - stuff;
/*
* If not enough vertical space, maximize annotation height while keeping
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.awt.dnd.DropTargetListener;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.concurrent.Semaphore;
import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.ActionMap;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.DefaultDesktopManager;
import javax.swing.DesktopManager;
+import javax.swing.InputMap;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import org.stackoverflowusers.file.WindowsShortcut;
+
/**
* Jalview Desktop
*
}
});
+ setKeyBindings(frame);
+
desktop.add(frame);
windowMenu.add(menuItem);
}
}
+ /**
+ * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
+ * the window
+ *
+ * @param frame
+ */
+ private static void setKeyBindings(JInternalFrame frame)
+ {
+ @SuppressWarnings("serial")
+ final Action closeAction = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ frame.dispose();
+ }
+ };
+
+ /*
+ * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action
+ */
+ KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ InputEvent.CTRL_DOWN_MASK);
+ KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+
+ InputMap inputMap = frame
+ .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
+ String ctrlW = ctrlWKey.toString();
+ inputMap.put(ctrlWKey, ctrlW);
+ inputMap.put(cmdWKey, ctrlW);
+
+ ActionMap actionMap = frame.getActionMap();
+ actionMap.put(ctrlW, closeAction);
+ }
+
@Override
public void lostOwnership(Clipboard clipboard, Transferable contents)
{
return groovyConsole;
}
+ /**
+ * handles the payload of a drag and drop event.
+ *
+ * TODO refactor to desktop utilities class
+ *
+ * @param files
+ * - Data source strings extracted from the drop event
+ * @param protocols
+ * - protocol for each data source extracted from the drop event
+ * @param evt
+ * - the drop event
+ * @param t
+ * - the payload from the drop event
+ * @throws Exception
+ */
public static void transferFromDropTarget(List<String> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
Transferable t) throws Exception
{
DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
+ "text/uri-list;class=java.lang.String"), urlFlavour = null;
+ try
+ {
+ urlFlavour = new DataFlavor(
+ "application/x-java-url; class=java.net.URL");
+ } catch (ClassNotFoundException cfe)
+ {
+ Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ }
+
+ if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
+ {
+
+ try
+ {
+ java.net.URL url = (URL) t.getTransferData(urlFlavour);
+ // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
+ // means url may be null.
+ if (url != null)
+ {
+ protocols.add(DataSourceType.URL);
+ files.add(url.toString());
+ Cache.log.debug("Drop handled as URL dataflavor "
+ + files.get(files.size() - 1));
+ return;
+ }
+ else
+ {
+ if (Platform.isAMac())
+ {
+ System.err.println(
+ "Please ignore plist error - occurs due to problem with java 8 on OSX");
+ }
+ ;
+ }
+ } catch (Throwable ex)
+ {
+ Cache.log.debug("URL drop handler failed.", ex);
+ }
+ }
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
// Works on Windows and MacOSX
// fallback to text: workaround - on OSX where there's a JVM bug
Cache.log.debug("standard URIListFlavor failed. Trying text");
// try text fallback
- data = (String) t.getTransferData(
- new DataFlavor("text/plain;class=java.lang.String"));
- if (Cache.log.isDebugEnabled())
+ DataFlavor textDf = new DataFlavor(
+ "text/plain;class=java.lang.String");
+ if (t.isDataFlavorSupported(textDf))
{
- Cache.log.debug("fallback returned " + data);
+ data = (String) t.getTransferData(textDf);
}
+
+ Cache.log.debug("Plain text drop content returned "
+ + (data == null ? "Null - failed" : data));
+
}
- while (protocols.size() < files.size())
- {
- Cache.log.debug("Adding missing FILE protocol for "
- + files.get(protocols.size()));
- protocols.add(DataSourceType.FILE);
- }
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data, "\r\n"); st.hasMoreTokens();)
+ if (data != null)
{
- added = true;
- String s = st.nextToken();
- if (s.startsWith("#"))
+ while (protocols.size() < files.size())
{
- // the line is a comment (as per the RFC 2483)
- continue;
- }
- java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase().startsWith("http"))
- {
- protocols.add(DataSourceType.URL);
- files.add(uri.toString());
+ Cache.log.debug("Adding missing FILE protocol for "
+ + files.get(protocols.size()));
+ protocols.add(DataSourceType.FILE);
}
- else
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data, "\r\n"); st.hasMoreTokens();)
{
- // otherwise preserve old behaviour: catch all for file objects
- java.io.File file = new java.io.File(uri);
- protocols.add(DataSourceType.FILE);
- files.add(file.toString());
+ added = true;
+ String s = st.nextToken();
+ if (s.startsWith("#"))
+ {
+ // the line is a comment (as per the RFC 2483)
+ continue;
+ }
+ java.net.URI uri = new java.net.URI(s);
+ if (uri.getScheme().toLowerCase().startsWith("http"))
+ {
+ protocols.add(DataSourceType.URL);
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ protocols.add(DataSourceType.FILE);
+ files.add(file.toString());
+ }
}
}
+
if (Cache.log.isDebugEnabled())
{
if (data == null || !added)
{
- Cache.log.debug(
- "Couldn't resolve drop data. Here are the supported flavors:");
- for (DataFlavor fl : t.getTransferDataFlavors())
+
+ if (t.getTransferDataFlavors() != null
+ && t.getTransferDataFlavors().length > 0)
{
Cache.log.debug(
- "Supported transfer dataflavor: " + fl.toString());
- Object df = t.getTransferData(fl);
- if (df != null)
+ "Couldn't resolve drop data. Here are the supported flavors:");
+ for (DataFlavor fl : t.getTransferDataFlavors())
{
- Cache.log.debug("Retrieves: " + df);
- }
- else
- {
- Cache.log.debug("Retrieved nothing");
+ Cache.log.debug(
+ "Supported transfer dataflavor: " + fl.toString());
+ Object df = t.getTransferData(fl);
+ if (df != null)
+ {
+ Cache.log.debug("Retrieves: " + df);
+ }
+ else
+ {
+ Cache.log.debug("Retrieved nothing");
+ }
}
}
+ else
+ {
+ Cache.log.debug("Couldn't resolve dataflavor for drop: "
+ + t.toString());
+ }
+ }
+ }
+ }
+ if (Platform.isWindows())
+
+ {
+ Cache.log.debug("Scanning dropped content for Windows Link Files");
+
+ // resolve any .lnk files in the file drop
+ for (int f = 0; f < files.size(); f++)
+ {
+ String source = files.get(f).toLowerCase();
+ if (protocols.get(f).equals(DataSourceType.FILE)
+ && (source.endsWith(".lnk") || source.endsWith(".url")
+ || source.endsWith(".site")))
+ {
+ try {
+ File lf = new File(files.get(f));
+ // process link file to get a URL
+ Cache.log.debug("Found potential link file: " + lf);
+ WindowsShortcut wscfile = new WindowsShortcut(lf);
+ String fullname = wscfile.getRealFilename();
+ protocols.set(f, FormatAdapter.checkProtocol(fullname));
+ files.set(f, fullname);
+ Cache.log.debug("Parsed real filename " + fullname
+ + " to extract protocol: " + protocols.get(f));
+ }
+ catch (Exception ex)
+ {
+ Cache.log.error("Couldn't parse "+files.get(f)+" as a link file.",ex);
+ }
}
}
}
*/
package jalview.gui;
+import jalview.bin.Cache;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
import jalview.util.MessageManager;
import jalview.ws.jws2.dm.JabaOption;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.ParameterI;
import jalview.ws.params.ValueConstrainI;
import jalview.ws.params.ValueConstrainI.ValueType;
+import jalview.ws.params.simple.FileParameter;
import jalview.ws.params.simple.LogarithmicParameter;
+import jalview.ws.params.simple.RadioChoiceParameter;
import jalview.ws.params.simple.StringParameter;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
+import java.awt.Container;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.event.ActionListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
+import java.io.File;
import java.net.URL;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
+import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSlider;
import javax.swing.JTextArea;
boolean adjusting;
+ /*
+ * drop-down list of choice options (if applicable)
+ */
JComboBox<String> choicebox;
+ /*
+ * radio buttons as an alternative to combo box
+ */
+ ButtonGroup buttonGroup;
+
JPanel controlsPanel = new JPanel();
boolean descriptionIsVisible = false;
{
ValueType type = validator.getType();
isIntegerParameter = type == ValueType.Integer;
- isStringParameter = type == ValueType.String;
+ isStringParameter = type == ValueType.String
+ || type == ValueType.File;
/*
* ensure slider has an integer range corresponding to
{
return;
}
- if (!isChoiceParameter)
- {
- updateSliderFromValueField();
- }
checkIfModified();
}
public ArgumentI getParameter()
{
ParameterI prm = parameter.copy();
- if (isChoiceParameter)
+ String value = null;
+ if (parameter instanceof RadioChoiceParameter)
+ {
+ value = buttonGroup.getSelection().getActionCommand();
+ }
+ else if (isChoiceParameter)
{
- String value = getSelectedValue(this.parameter, choicebox.getSelectedIndex());
- prm.setValue(value);
+ value = getSelectedValue(this.parameter,
+ choicebox.getSelectedIndex());
}
else
{
- prm.setValue(valueField.getText());
+ value = valueField.getText();
}
+ prm.setValue(value);
+
return prm;
}
void updateControls(ParameterI parm)
{
adjusting = true;
- boolean init = (choicebox == null && valueField == null);
+ boolean init = (choicebox == null && valueField == null
+ && buttonGroup == null);
if (init)
{
- if (isChoiceParameter)
+ if (parm instanceof RadioChoiceParameter)
+ {
+ buttonGroup = addRadioButtons(parameter, controlsPanel);
+ }
+ else if (isChoiceParameter)
{
choicebox = buildComboBox(parm);
choicebox.addActionListener(this);
}
});
valueField.setPreferredSize(new Dimension(65, 25));
+ if (parm instanceof FileParameter)
+ {
+ valueField.setToolTipText(MessageManager
+ .getString("label.double_click_to_browse"));
+ valueField.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String dir = Cache.getProperty("LAST_DIRECTORY");
+ JalviewFileChooser chooser = new JalviewFileChooser(dir);
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(
+ MessageManager.getString("action.select_ddbb"));
+
+ int val = chooser.showOpenDialog(ParamBox.this);
+ if (val == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File choice = chooser.getSelectedFile();
+ String path = choice.getPath();
+ valueField.setText(path);
+ Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ FileLoader.updateRecentlyOpened(path,
+ DataSourceType.FILE);
+ }
+ }
+ }
+ });
+ }
+
controlsPanel.add(slider, BorderLayout.WEST);
controlsPanel.add(valueField, BorderLayout.EAST);
}
{
if (isChoiceParameter)
{
- choicebox.setSelectedItem(value);
+ if (!(parm instanceof RadioChoiceParameter))
+ {
+ choicebox.setSelectedItem(value);
+ }
}
else
{
}
/**
+ * Adds a panel to comp, containing a label and radio buttons for the choice
+ * of values of the given option. Returns a ButtonGroup whose members are
+ * the added radio buttons.
+ *
+ * @param option
+ * @param comp
+ *
+ * @return
+ */
+ protected ButtonGroup addRadioButtons(OptionI option, Container comp)
+ {
+ ButtonGroup bg = new ButtonGroup();
+ JPanel radioPanel = new JPanel();
+ radioPanel.add(new JLabel(option.getDescription()));
+
+ String value = option.getValue();
+
+ for (String opt : option.getPossibleValues())
+ {
+ JRadioButton btn = new JRadioButton(opt);
+ btn.setActionCommand(opt);
+ boolean selected = opt.equals(value);
+ btn.setSelected(selected);
+ btn.addActionListener(this);
+ bg.add(btn);
+ radioPanel.add(btn);
+ }
+ comp.add(radioPanel);
+
+ return bg;
+ }
+
+ /**
* Action depends on the type of the input parameter:
* <ul>
* <li>if a text input, returns the trimmed value</li>
- * <li>if a choice list, returns the selected value</li>
+ * <li>if a choice list or radio button, returns the selected value</li>
* <li>if a value slider and input field, sets the value of the slider from
* the value in the text field, limiting it to any defined min-max
* range.</li>
{
if (isChoiceParameter)
{
- return getSelectedValue(this.parameter, choicebox.getSelectedIndex());
+ if (parameter instanceof RadioChoiceParameter)
+ {
+ return buttonGroup.getSelection().getActionCommand();
+ }
+ else
+ {
+ return getSelectedValue(this.parameter,
+ choicebox.getSelectedIndex());
+ }
}
slider.setVisible(false);
return valueField.getText().trim();
* @param opt
* @return
*/
- protected JComboBox<String> buildComboBox(OptionI opt)
+ protected static JComboBox<String> buildComboBox(OptionI opt)
{
JComboBox<String> cb = null;
List<String> displayNames = opt.getDisplayNames();
return cb;
}
- /*
+ /**
* Answers the value corresponding to the selected item in the choice combo
- * box. If display names were not provided, this is simply the selected
- * value. If display names were provided, it is the value corresponding to
- * the selected item index.
+ * box. Note that this returns the underlying value even if a different
+ * display name is used in the combo box.
*
* @return
*/
// one value is actually returned even if this.val is not displayed
value = possibleValues.get(0);
}
- else
+ else if (sel >= 0 && sel < possibleValues.size())
{
- if (sel >= 0 && sel < possibleValues.size())
- {
- value = possibleValues.get(sel);
- }
- else
- {
- value = opt.getValue();
- }
+ value = possibleValues.get(sel);
}
return value;
}
ViewportRanges ranges = av.getRanges();
ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues);
+ // we need to call this again to make sure the startColumn +
+ // wrappedWidthInResidues values are used to calculate wrappedVisibleWidths
+ // correctly.
+ calculateWrappedGeometry(canvasWidth, canvasHeight);
+
/*
* draw one width at a time (including any scales or annotation shown),
* until we have run out of either alignment or vertical space available
import jalview.ws.params.WsParamSetI;
import jalview.ws.params.simple.BooleanOption;
import jalview.ws.params.simple.DoubleParameter;
+import jalview.ws.params.simple.FileParameter;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.LogarithmicParameter;
import jalview.ws.params.simple.Option;
+import jalview.ws.params.simple.RadioChoiceParameter;
import jalview.ws.params.simple.StringParameter;
import java.io.File;
args.add(new BooleanOption(
MessageManager.getString(HMMSearch.AUTO_ALIGN_SEQS_KEY),
MessageManager.getString("label.auto_align_seqs_desc"), false,
- false, true, null));
+ false, false, null));
args.add(new BooleanOption(
MessageManager.getString(HMMSearch.USE_ACCESSIONS_KEY),
MessageManager.getString("label.use_accessions_desc"), false,
*/
addChoiceOfHmm(args);
- addChoiceOfDatabase(args);
-
+ // addChoiceOfDatabase(args);
+
+ String thisAlignment = MessageManager
+ .getString(HMMSearch.THIS_ALIGNMENT_KEY);
+ String database = MessageManager.getString("label.database");
+ args.add(new RadioChoiceParameter(
+ MessageManager.getString("action.search"), null,
+ Arrays.asList(thisAlignment,
+ database),
+ thisAlignment));
+ args.add(new FileParameter(database, "", false, "", ""));
args.add(new IntegerParameter(
MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
MessageManager.getString("label.number_of_results_desc"), true,
100, 0, 100000));
- args.add(new StringParameter(
+ args.add(new RadioChoiceParameter(
MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
- true, HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_NONE,
Arrays.asList(HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_EVALUE,
HMMSearch.CUTOFF_SCORE),
- null));
+ HMMSearch.CUTOFF_EVALUE));
args.add(new LogarithmicParameter(
MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
MessageManager.getString("label.seq_e_value_desc"), false, 1D,
String seqScoreCutoff = null;
String domScoreCutoff = null;
databaseName = "Alignment";
+ boolean searchAlignment = false;
if (params != null)
{
{
seqsToReturn = Integer.parseInt(arg.getValue());
}
+ else if (MessageManager.getString("action.search").equals(name))
+ {
+ searchAlignment = arg.getValue().equals(
+ MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
+ }
+ else if (MessageManager.getString(DATABASE_KEY).equals(name))
+ {
+ dbPath = arg.getValue();
+ int pos = dbPath.lastIndexOf(File.separator);
+ databaseName = dbPath.substring(pos + 1);
+ databaseFile = new File(dbPath);
+ }
else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
.equals(name))
{
args.add(domScoreCutoff);
}
- if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
- .equals(dbPath))
+// if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
+// .equals(dbPath))
+ if (searchAlignment)
{
/*
* no external database specified for search, so
long end;
- private boolean parseCalled;
+ /**
+ * true if parse() has been called
+ */
+ private boolean parseCalled = false;
+
+ private boolean parseImmediately = true;
+
+ /**
+ * @return if doParse() was called at construction time
+ */
+ protected boolean isParseImmediately()
+ {
+ return parseImmediately;
+ }
/**
* Creates a new AlignFile object.
{
super(source);
initData();
+
+ // stash flag in case parse needs to know if it has to autoconfigure or was
+ // configured after construction
+ this.parseImmediately = parseImmediately;
+
if (parseImmediately)
{
doParse();
import jalview.util.Format;
import java.io.IOException;
-import java.util.Hashtable;
+import java.util.HashMap;
+import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
{
int i = 0;
boolean flag = false;
- boolean rna = false;
boolean top = false;
- StringBuffer pssecstr = new StringBuffer(),
- consstr = new StringBuffer();
- Vector headers = new Vector();
- Hashtable seqhash = new Hashtable();
+ StringBuffer pssecstr = new StringBuffer();
+ StringBuffer consstr = new StringBuffer();
+ Vector<String> headers = new Vector<>();
+ Map<String, StringBuffer> seqhash = new HashMap<>();
StringBuffer tempseq;
String line, id;
StringTokenizer str;
{
top = true;
}
- if (line.indexOf(" ") != 0)
+ boolean isConservation = line.startsWith(SPACE)
+ || line.startsWith(TAB);
+ if (!isConservation)
{
- str = new StringTokenizer(line, " ");
+ str = new StringTokenizer(line);
if (str.hasMoreTokens())
{
{
if (seqhash.containsKey(id))
{
- tempseq = (StringBuffer) seqhash.get(id);
+ tempseq = seqhash.get(id);
}
else
{
AlignmentAnnotation lastssa = null;
if (pssecstr.length() == maxLength)
{
- Vector ss = new Vector();
+ Vector<AlignmentAnnotation> ss = new Vector<>();
AlignmentAnnotation ssa = lastssa = StockholmFile
.parseAnnotationRow(ss, "secondary structure",
pssecstr.toString());
}
if (consstr.length() == maxLength)
{
- Vector ss = new Vector();
+ Vector<AlignmentAnnotation> ss = new Vector<>();
AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
"secondary structure", consstr.toString());
ssa.label = "Consensus Secondary Structure";
out.append(new Format("%-" + maxid + "s")
.form(printId(s[j], jvsuffix) + " "));
- int start = i * len;
- int end = start + len;
+ int chunkStart = i * len;
+ int chunkEnd = chunkStart + len;
int length = s[j].getLength();
- if ((end < length) && (start < length))
+ if ((chunkEnd < length) && (chunkStart < length))
{
- out.append(s[j].getSequenceAsString(start, end));
+ out.append(s[j].getSequenceAsString(chunkStart, chunkEnd));
}
else
{
- if (start < length)
+ if (chunkStart < length)
{
- out.append(s[j].getSequenceAsString().substring(start));
+ out.append(s[j].getSequenceAsString().substring(chunkStart));
}
}
private static final String NOTE = "Note";
- protected static final String TAB = "\t";
-
protected static final String GFF_VERSION = "##gff-version";
private AlignmentI lastmatchedAl = null;
import java.io.File;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
import java.util.StringTokenizer;
-import java.util.Vector;
import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
+ private static final String TAB = "\t";
+
String file;
DataSourceType protocol;
}
}
- public void updateRecentlyOpened()
+ /**
+ * Updates (or creates) the tab-separated list of recently opened files held
+ * under the given property name by inserting the filePath at the front of the
+ * list. Duplicates are removed, and the list is limited to 11 entries. The
+ * method returns the updated value of the property.
+ *
+ * @param filePath
+ * @param sourceType
+ */
+ public static String updateRecentlyOpened(String filePath,
+ DataSourceType sourceType)
{
- Vector recent = new Vector();
- if (protocol == DataSourceType.PASTE)
+ if (sourceType != DataSourceType.FILE
+ && sourceType != DataSourceType.URL)
{
- // do nothing if the file was pasted in as text... there is no filename to
- // refer to it as.
- return;
+ return null;
}
- if (file != null
- && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+
+ String propertyName = sourceType == DataSourceType.FILE ? "RECENT_FILE"
+ : "RECENT_URL";
+ String historyItems = Cache.getProperty(propertyName);
+ if (filePath != null
+ && filePath.indexOf(System.getProperty("java.io.tmpdir")) > -1)
{
// ignore files loaded from the system's temporary directory
- return;
+ return null;
}
- String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
- : "RECENT_URL";
- String historyItems = jalview.bin.Cache.getProperty(type);
-
- StringTokenizer st;
+ List<String> recent = new ArrayList<>();
if (historyItems != null)
{
- st = new StringTokenizer(historyItems, "\t");
+ StringTokenizer st = new StringTokenizer(historyItems, TAB);
while (st.hasMoreTokens())
{
- recent.addElement(st.nextElement().toString().trim());
+ String trimmed = st.nextToken().trim();
+ if (!recent.contains(trimmed))
+ {
+ recent.add(trimmed);
+ }
}
}
- if (recent.contains(file))
+ /*
+ * if file was already in the list, it moves to the top
+ */
+ if (recent.contains(filePath))
{
- recent.remove(file);
+ recent.remove(filePath);
}
- StringBuffer newHistory = new StringBuffer(file);
+ StringBuilder newHistory = new StringBuilder(filePath);
for (int i = 0; i < recent.size() && i < 10; i++)
{
- newHistory.append("\t");
- newHistory.append(recent.elementAt(i));
+ newHistory.append(TAB);
+ newHistory.append(recent.get(i));
}
- Cache.setProperty(type, newHistory.toString());
+ String newProperty = newHistory.toString();
+ Cache.setProperty(propertyName, newProperty);
- if (protocol == DataSourceType.FILE)
- {
- Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
- }
+ return newProperty;
}
@Override
}
}
- updateRecentlyOpened();
+ updateRecentlyOpened(file, protocol);
+
+ if (protocol == DataSourceType.FILE && format != null)
+ {
+ Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
+ }
} catch (Exception er)
{
*/
public class FileParse
{
+ protected static final String SPACE = " ";
+
+ protected static final String TAB = "\t";
+
/**
* text specifying source of data. usually filename or url.
*/
}
}
});
- hmmSearch.add(hmmSearchSettings);
hmmSearch.add(hmmSearchRun);
- hmmSearch.add(addDatabase);
+ hmmSearch.add(hmmSearchSettings);
+ // hmmSearch.add(addDatabase);
/*
* top level menu
MessageManager.getString("label.default_browser_unix"));
defaultBrowser.setFont(LABEL_FONT);
defaultBrowser.setText("");
-
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.double_click_to_browse"));
+ defaultBrowser.setToolTipText(tooltip);
defaultBrowser.addMouseListener(new MouseAdapter()
{
@Override
pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
pathLabel.setText(MessageManager.getString("label.chimera_path"));
- 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(LABEL_FONT);
chimeraPath.setText("");
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_path_tip"));
+ chimeraPath.setToolTipText(tooltip);
chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
chimeraPath.addMouseListener(new MouseAdapter()
{
startupCheckbox.setSelected(true);
startupFileTextfield.setFont(LABEL_FONT);
startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
+ final String tooltip = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.double_click_to_browse"));
+ startupFileTextfield.setToolTipText(tooltip);
startupFileTextfield.addMouseListener(new MouseAdapter()
{
@Override
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
{
// FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
- pdb = new JmolParser(pdbFile, sourceType);
-
+ pdb = new JmolParser(false, pdbFile, sourceType);
+ pdb.addSettings(parseSecStr && processSecondaryStructure,
+ parseSecStr && addTempFacAnnot,
+ parseSecStr && secStructServices);
+ pdb.doParse();
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& DataSourceType.FILE == sourceType)
{
import java.io.File;
import java.io.IOException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.FileSystems;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.PathMatcher;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
/**
* Miscellaneous file-related functions
return f;
}
+ /**
+ * Answers a (possibly empty) list of file paths found by searching below
+ * <code>from</code> that match the supplied regular expression
+ * <code>pattern</code>. Results may include <code>from</code> itself if it
+ * matches. If an exception occurs it is written to syserr and any results up to
+ * that point are returned. Note that the regular expression match applies to
+ * the whole path of any matched file.
+ * <p>
+ * WARNING: because the whole directory tree below <code>from</code> is
+ * searched, this method may be slow if used for a high level directory, or may
+ * exit prematurely if security or other exceptions occur.
+ *
+ * <pre>
+ * Example:
+ * findMatchingPaths(Paths.get("C:/Program Files"), ".*/chimera.exe$")
+ * </pre>
+ *
+ * @param from
+ * @param pattern
+ *
+ * @return
+ * @see https://stackoverflow.com/questions/794381/how-to-find-files-that-match-a-wildcard-string-in-java/31685610#comment62441832_31685610
+ */
+ public static List<String> findMatchingPaths(Path from, String pattern)
+ {
+ List<String> matches = new ArrayList<>();
+ PathMatcher pathMatcher = FileSystems.getDefault()
+ .getPathMatcher("regex:" + pattern);
+ try
+ {
+ Files.walk(from).filter(pathMatcher::matches)
+ .forEach(m -> matches.add(m.toString()));
+ } catch (IOException e)
+ {
+ System.err.println(
+ "Error searching for " + pattern + " : " + e.toString());
+ }
+
+ return matches;
+ }
+
+ /**
+ * Answers a (possibly empty) list of paths to files below the given root path,
+ * that match the given pattern. The pattern should be a '/' delimited set of
+ * glob patterns, each of which is used to match child file names (not full
+ * paths). Note that 'directory spanning' glob patterns (**) are <em>not</em>
+ * supported by this method.
+ * <p>
+ * For example
+ *
+ * <pre>
+ * findMatches("C:\\", "Program Files*/Chimera*/bin/{chimera,chimera.exe}"
+ * </pre>
+ *
+ * would match "C:\Program Files\Chimera 1.11\bin\chimera.exe" and "C:\Program
+ * Files (x86)\Chimera 1.10.1\bin\chimera"
+ *
+ * @param root
+ * @param pattern
+ * @return
+ * @see https://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob
+ */
+ public static List<String> findMatches(String root, String pattern)
+ {
+ List<String> results = new ArrayList<>();
+ try
+ {
+ Path from = Paths.get(root);
+ findMatches(results, from, Arrays.asList(pattern.split("/")));
+ } catch (Throwable e)
+ {
+ // Paths.get can throw IllegalArgumentException
+ System.err.println(String.format("Error searching %s for %s: %s",
+ root, pattern, e.toString()));
+ }
+
+ return results;
+ }
+
+ /**
+ * A helper method that performs recursive search of file patterns and adds any
+ * 'leaf node' matches to the results list
+ *
+ * @param results
+ * @param from
+ * @param patterns
+ */
+ protected static void findMatches(List<String> results, Path from,
+ List<String> patterns)
+ {
+ if (patterns.isEmpty())
+ {
+ /*
+ * reached end of recursion with all components matched
+ */
+ results.add(from.toString());
+ return;
+ }
+
+ String pattern = patterns.get(0);
+ try (DirectoryStream<Path> dirStream = Files.newDirectoryStream(from,
+ pattern))
+ {
+ dirStream.forEach(p -> {
+
+ /*
+ * matched a next level file - search below it
+ * (ignore non-directory non-leaf matches)
+ */
+ List<String> subList = patterns.subList(1, patterns.size());
+ if (subList.isEmpty() || p.toFile().isDirectory())
+ {
+ findMatches(results, p, subList);
+ }
+ });
+ } catch (IOException e)
+ {
+ System.err.println(String.format("Error searching %s: %s", pattern,
+ e.toString()));
+ }
+ }
}
public enum ValueType
{
- Integer, Float, String, Double
+ Integer, Float, String, Double, File
};
ValueType getType();
--- /dev/null
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ValueConstrainI;
+
+/**
+ * A class that represents a file parameter. User entry options should include
+ * direct input of a file path as text, or file selection using a file browser.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class FileParameter extends StringParameter
+{
+
+ public FileParameter(String name, String description, boolean required,
+ String defValue, String value)
+ {
+ super(name, description, required, defValue, value);
+ }
+
+ @Override
+ public ValueConstrainI getValidValue()
+ {
+ return new ValueConstrainI()
+ {
+
+ @Override
+ public ValueType getType()
+ {
+ return ValueType.File;
+ }
+
+ @Override
+ public Number getMax()
+ {
+ return null;
+ }
+
+ @Override
+ public Number getMin()
+ {
+ return null;
+ }
+ };
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.ws.params.simple;
+
+import java.util.List;
+
+/**
+ * A parameter with a choice of possible options, preferred to be rendered as
+ * radio buttons if possible
+ */
+public class RadioChoiceParameter extends StringParameter
+{
+
+ /**
+ * Constructor
+ *
+ * @param name
+ * @param description
+ * @param options
+ * @param def
+ */
+ public RadioChoiceParameter(String name, String description,
+ List<String> options, String def)
+ {
+ super(name, description, true, def, def, options, null);
+ }
+}
--- /dev/null
+package org.stackoverflowusers.file;
+
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.text.ParseException;
+
+/**
+ * Represents a Windows shortcut (typically visible to Java only as a '.lnk' file).
+ *
+ * Retrieved 2011-09-23 from http://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java/672775#672775
+ * Originally called LnkParser
+ *
+ * Written by: (the stack overflow users, obviously!)
+ * Apache Commons VFS dependency removed by crysxd (why were we using that!?) https://github.com/crysxd
+ * Headerified, refactored and commented by Code Bling http://stackoverflow.com/users/675721/code-bling
+ * Network file support added by Stefan Cordes http://stackoverflow.com/users/81330/stefan-cordes
+ * Adapted by Sam Brightman http://stackoverflow.com/users/2492/sam-brightman
+ * Based on information in 'The Windows Shortcut File Format' by Jesse Hager <jessehager@iname.com>
+ * And somewhat based on code from the book 'Swing Hacks: Tips and Tools for Killer GUIs'
+ * by Joshua Marinacci and Chris Adamson
+ * ISBN: 0-596-00907-0
+ * http://www.oreilly.com/catalog/swinghks/
+ */
+public class WindowsShortcut
+{
+ private boolean isDirectory;
+ private boolean isLocal;
+ private String real_file;
+
+ /**
+ * Provides a quick test to see if this could be a valid link !
+ * If you try to instantiate a new WindowShortcut and the link is not valid,
+ * Exceptions may be thrown and Exceptions are extremely slow to generate,
+ * therefore any code needing to loop through several files should first check this.
+ *
+ * @param file the potential link
+ * @return true if may be a link, false otherwise
+ * @throws IOException if an IOException is thrown while reading from the file
+ */
+ public static boolean isPotentialValidLink(File file) throws IOException {
+ final int minimum_length = 0x64;
+ InputStream fis = new FileInputStream(file);
+ boolean isPotentiallyValid = false;
+ try {
+ isPotentiallyValid = file.isFile()
+ && file.getName().toLowerCase().endsWith(".lnk")
+ && fis.available() >= minimum_length
+ && isMagicPresent(getBytes(fis, 32));
+ } finally {
+ fis.close();
+ }
+ return isPotentiallyValid;
+ }
+
+ public WindowsShortcut(File file) throws IOException, ParseException {
+ InputStream in = new FileInputStream(file);
+ try {
+ parseLink(getBytes(in));
+ } finally {
+ in.close();
+ }
+ }
+
+ /**
+ * @return the name of the filesystem object pointed to by this shortcut
+ */
+ public String getRealFilename() {
+ return real_file;
+ }
+
+ /**
+ * Tests if the shortcut points to a local resource.
+ * @return true if the 'local' bit is set in this shortcut, false otherwise
+ */
+ public boolean isLocal() {
+ return isLocal;
+ }
+
+ /**
+ * Tests if the shortcut points to a directory.
+ * @return true if the 'directory' bit is set in this shortcut, false otherwise
+ */
+ public boolean isDirectory() {
+ return isDirectory;
+ }
+
+ /**
+ * Gets all the bytes from an InputStream
+ * @param in the InputStream from which to read bytes
+ * @return array of all the bytes contained in 'in'
+ * @throws IOException if an IOException is encountered while reading the data from the InputStream
+ */
+ private static byte[] getBytes(InputStream in) throws IOException {
+ return getBytes(in, null);
+ }
+
+ /**
+ * Gets up to max bytes from an InputStream
+ * @param in the InputStream from which to read bytes
+ * @param max maximum number of bytes to read
+ * @return array of all the bytes contained in 'in'
+ * @throws IOException if an IOException is encountered while reading the data from the InputStream
+ */
+ private static byte[] getBytes(InputStream in, Integer max) throws IOException {
+ // read the entire file into a byte buffer
+ ByteArrayOutputStream bout = new ByteArrayOutputStream();
+ byte[] buff = new byte[256];
+ while (max == null || max > 0) {
+ int n = in.read(buff);
+ if (n == -1) {
+ break;
+ }
+ bout.write(buff, 0, n);
+ if (max != null)
+ max -= n;
+ }
+ in.close();
+ return bout.toByteArray();
+ }
+
+ private static boolean isMagicPresent(byte[] link) {
+ final int magic = 0x0000004C;
+ final int magic_offset = 0x00;
+ return link.length >= 32 && bytesToDword(link, magic_offset) == magic;
+ }
+
+ /**
+ * Gobbles up link data by parsing it and storing info in member fields
+ * @param link all the bytes from the .lnk file
+ */
+ private void parseLink(byte[] link) throws ParseException {
+ try {
+ if (!isMagicPresent(link))
+ throw new ParseException("Invalid shortcut; magic is missing", 0);
+
+ // get the flags byte
+ byte flags = link[0x14];
+
+ // get the file attributes byte
+ final int file_atts_offset = 0x18;
+ byte file_atts = link[file_atts_offset];
+ byte is_dir_mask = (byte)0x10;
+ if ((file_atts & is_dir_mask) > 0) {
+ isDirectory = true;
+ } else {
+ isDirectory = false;
+ }
+
+ // if the shell settings are present, skip them
+ final int shell_offset = 0x4c;
+ final byte has_shell_mask = (byte)0x01;
+ int shell_len = 0;
+ if ((flags & has_shell_mask) > 0) {
+ // the plus 2 accounts for the length marker itself
+ shell_len = bytesToWord(link, shell_offset) + 2;
+ }
+
+ // get to the file settings
+ int file_start = 0x4c + shell_len;
+
+ final int file_location_info_flag_offset_offset = 0x08;
+ int file_location_info_flag = link[file_start + file_location_info_flag_offset_offset];
+ isLocal = (file_location_info_flag & 2) == 0;
+ // get the local volume and local system values
+ //final int localVolumeTable_offset_offset = 0x0C;
+ final int basename_offset_offset = 0x10;
+ final int networkVolumeTable_offset_offset = 0x14;
+ final int finalname_offset_offset = 0x18;
+ int finalname_offset = link[file_start + finalname_offset_offset] + file_start;
+ String finalname = getNullDelimitedString(link, finalname_offset);
+ if (isLocal) {
+ int basename_offset = link[file_start + basename_offset_offset] + file_start;
+ String basename = getNullDelimitedString(link, basename_offset);
+ real_file = basename + finalname;
+ } else {
+ int networkVolumeTable_offset = link[file_start + networkVolumeTable_offset_offset] + file_start;
+ int shareName_offset_offset = 0x08;
+ int shareName_offset = link[networkVolumeTable_offset + shareName_offset_offset]
+ + networkVolumeTable_offset;
+ String shareName = getNullDelimitedString(link, shareName_offset);
+ real_file = shareName + "\\" + finalname;
+ }
+ } catch (ArrayIndexOutOfBoundsException e) {
+ throw new ParseException("Could not be parsed, probably not a valid WindowsShortcut", 0);
+ }
+ }
+
+ private static String getNullDelimitedString(byte[] bytes, int off) {
+ int len = 0;
+ // count bytes until the null character (0)
+ while (true) {
+ if (bytes[off + len] == 0) {
+ break;
+ }
+ len++;
+ }
+ return new String(bytes, off, len);
+ }
+
+ /*
+ * convert two bytes into a short note, this is little endian because it's
+ * for an Intel only OS.
+ */
+ private static int bytesToWord(byte[] bytes, int off) {
+ return ((bytes[off + 1] & 0xff) << 8) | (bytes[off] & 0xff);
+ }
+
+ private static int bytesToDword(byte[] bytes, int off) {
+ return (bytesToWord(bytes, off + 2) << 16) | bytesToWord(bytes, off);
+ }
+
+}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 static org.testng.Assert.assertEquals;
--- /dev/null
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+
+import org.testng.annotations.Test;
+
+public class ClustalFileTest
+{
+ @Test(groups="Functional")
+ public void testParse_withNumbering() throws IOException
+ {
+ //@formatter:off
+ String data = "CLUSTAL\n\n"
+ + "FER_CAPAA/1-8 -----------------------------------------------------------A\t1\n"
+ + "FER_CAPAN/1-55 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA 48\n"
+ + "FER1_SOLLC/1-55 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
+ + "Q93XJ9_SOLTU/1-55 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
+ + "FER1_PEA/1-60 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA 53\n\n"
+ + "FER_CAPAA/1-8 SYKVKLI 8\n"
+ + "FER_CAPAN/1-55 SYKVKLI 55\n"
+ + "FER1_SOLLC/1-55 SYKVKLI 55\n"
+ + "Q93XJ9_SOLTU/1-55 SYKVKLI 55\n"
+ + "FER1_PEA/1-60 SYKVKLV 60\n"
+ + " .* .:....*******..** ..........** ********...*:::* ...\n"
+ + "\t\t.:.::. *\n";
+ //@formatter:on
+ ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
+ cf.parse();
+ SequenceI[] seqs = cf.getSeqsAsArray();
+ assertEquals(seqs.length, 5);
+ assertEquals(seqs[0].getName(), "FER_CAPAA");
+ assertEquals(seqs[0].getStart(), 1);
+ assertEquals(seqs[0].getEnd(), 8);
+ assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
+ }
+
+ @Test(groups="Functional")
+ public void testParse_noNumbering() throws IOException
+ {
+ //@formatter:off
+ String data = "CLUSTAL\n\n"
+ + "FER_CAPAA/1-8 -----------------------------------------------------------A\n"
+ + "FER_CAPAN/1-55 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA\n"
+ + "FER1_SOLLC/1-55 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
+ + "Q93XJ9_SOLTU/1-55 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
+ + "FER1_PEA/1-60 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA\n\n"
+ + "FER_CAPAA/1-8 SYKVKLI\n"
+ + "FER_CAPAN/1-55 SYKVKLI\n"
+ + "FER1_SOLLC/1-55 SYKVKLI\n"
+ + "Q93XJ9_SOLTU/1-55 SYKVKLI\n"
+ + "FER1_PEA/1-60 SYKVKLV\n";
+ //@formatter:on
+ ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
+ cf.parse();
+ SequenceI[] seqs = cf.getSeqsAsArray();
+ assertEquals(seqs.length, 5);
+ assertEquals(seqs[0].getName(), "FER_CAPAA");
+ assertEquals(seqs[0].getStart(), 1);
+ assertEquals(seqs[0].getEnd(), 8);
+ assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
+ }
+}
package jalview.io;
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+
import org.junit.Assert;
import org.testng.annotations.Test;
// Data source type expected to be DataSourceType.URL
Assert.assertEquals(DataSourceType.URL, fileLoader.protocol);
}
+
+ @Test(groups = "Functional")
+ public void testUpdateRecentlyOpened()
+ {
+ // ensure properties file is read-only
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+
+ String recent = "RECENT_FILE";
+ Cache.removeProperty(recent);
+
+ String prop = FileLoader.updateRecentlyOpened("a/b/c",
+ DataSourceType.FILE);
+ assertEquals(prop, "a/b/c");
+
+ prop = FileLoader.updateRecentlyOpened("d/e/f", DataSourceType.FILE);
+ assertEquals(prop, "d/e/f\ta/b/c");
+
+ // revisiting a file moves it to the top of the list
+ prop = FileLoader.updateRecentlyOpened("a/b/c", DataSourceType.FILE);
+ assertEquals(prop, "a/b/c\td/e/f");
+
+ // history list is limited to the most recent 11 items
+ for (int i = 0; i < 20; i++)
+ {
+ prop = FileLoader.updateRecentlyOpened(String.format("%d.fa", i),
+ DataSourceType.FILE);
+ }
+ assertEquals(prop,
+ "19.fa\t18.fa\t17.fa\t16.fa\t15.fa\t14.fa\t13.fa\t12.fa\t11.fa\t10.fa\t9.fa");
+ }
}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.renderer;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.renderer.seqfeatures;
import static org.testng.Assert.assertEquals;
@Test(groups = { "Functional" })
public void compareTransferredToRefPDBAnnot() throws Exception
{
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
StructureImportSettings.setShowSeqFeatures(true);
AlignFrame ref = new FileLoader(false)
.LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.structure;
import static org.testng.Assert.assertEquals;
--- /dev/null
+package jalview.util;
+
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class FileUtilsTest
+{
+ @Test(groups = "Functional")
+ public void testFindMatchingPaths() throws IOException
+ {
+ String expect1 = Paths.get("..", "jalview", "examples", "plantfdx.fa")
+ .toString();
+ String expect2 = Paths.get("../jalview/examples/plantfdx.features")
+ .toString();
+ String expect3 = Paths
+ .get("../jalview/examples/testdata/plantfdx.features")
+ .toString();
+
+ List<String> matches = FileUtils
+ .findMatchingPaths(Paths.get(".."),
+ ".*[/\\\\]plant.*\\.f.*");
+ System.out.println(matches);
+ assertTrue(matches.contains(expect1));
+ assertTrue(matches.contains(expect2));
+ assertTrue(matches.contains(expect3));
+ }
+
+ @Test(groups = "External")
+ public void testWindowsPath() throws IOException
+ {
+ if (System.getProperty("os.name").startsWith("Windows"))
+ {
+ /*
+ * should pass provided Eclipse is installed
+ */
+ List<String> matches = FileUtils.findMatches("C:\\",
+ "Program Files*/eclips*/eclips?.exe");
+ assertFalse(matches.isEmpty());
+
+ /*
+ * should pass provided Chimera is installed
+ */
+ matches = FileUtils.findMatches("C:\\",
+ "Program Files*/Chimera*/bin/{chimera,chimera.exe}");
+ assertFalse(matches.isEmpty());
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testFindMatches() throws IOException
+ {
+ String expect1 = Paths.get("..", "jalview", "examples", "plantfdx.fa")
+ .toString();
+ String expect2 = Paths.get("../jalview/examples/plantfdx.features")
+ .toString();
+ String expect3 = Paths
+ .get("../jalview/examples/testdata/plantfdx.features")
+ .toString();
+
+ List<String> matches = FileUtils
+ .findMatches("..", "jalview/ex*/plant*.f*");
+ System.out.println(matches);
+ assertTrue(matches.contains(expect1));
+ assertTrue(matches.contains(expect2));
+ assertFalse(matches.contains(expect3));
+ }
+}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.ws.dbsources;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.ws.dbsources;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.ws.dbsources;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.ws.dbsources;
import static org.testng.Assert.assertEquals;
+ "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
+ "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
+ "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
+ + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+ + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
+ "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
+ "</uniprot>";
* Check sequence features
*/
Vector<UniprotFeature> features = entry.getFeature();
- assertEquals(3, features.size());
+ assertEquals(6, features.size());
UniprotFeature sf = features.get(0);
assertEquals("signal peptide", sf.getType());
assertNull(sf.getDescription());
assertEquals(21, sf.getBegin());
assertEquals(247, sf.getEnd());
+ sf = features.get(3);
+ assertEquals("sequence variant", sf.getType());
+ assertEquals("Variation: 'L' Original: 'M'", sf.getDescription());
+ assertEquals(41, sf.getPosition());
+ assertEquals(41, sf.getBegin());
+ assertEquals(41, sf.getEnd());
+
+ sf = features.get(4);
+ assertEquals("sequence variant", sf.getType());
+ assertEquals("Pathogenic Variation: 'L' Original: 'M'",
+ sf.getDescription());
+ assertEquals(41, sf.getPosition());
+ assertEquals(41, sf.getBegin());
+ assertEquals(41, sf.getEnd());
+
+ sf = features.get(5);
+ assertEquals("sequence variant", sf.getType());
+ assertEquals("Pathogenic Original: 'M'", sf.getDescription());
+ assertEquals(41, sf.getPosition());
+ assertEquals(41, sf.getBegin());
+ assertEquals(41, sf.getEnd());
/*
* Check cross-references
*/
<string><![CDATA[logo.gif]]></string>
</property>
<property name="smallIconPath">
- <string><![CDATA[/home/cruisecontrol/jalview/resources/images/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/resources/images/]]></string>
</property>
<property name="largeIconPath">
- <string><![CDATA[/home/cruisecontrol/jalview/resources/images/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/resources/images/]]></string>
</property>
<property name="macOSXIconPath">
- <string><![CDATA[/home/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
</property>
<property name="macOSXIconName">
<string><![CDATA[mac_logo.icns]]></string>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/dist/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/dist/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<string><![CDATA[The installer cannot run on your configuration. It will now quit.]]></string>
</property>
<property name="userSplashPath">
- <string><![CDATA[/home/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
</property>
<property name="userSplashName">
<string><![CDATA[jalview.gif]]></string>
<boolean>true</boolean>
</property>
<property name="buildOutputLocation">
- <string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/utils/InstallAnywhere/Jalview_Build_Output]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/utils/InstallAnywhere/Jalview_Build_Output]]></string>
</property>
<property name="relatedProjectSettings">
<object class="com.zerog.ia.installer.RelatedProjectSettings" objectID="97f2363da6ac">
<boolean>true</boolean>
</property>
<property name="backgroundImagePath">
- <string><![CDATA[/home/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
</property>
<property name="backgroundImageName">
<string><![CDATA[align.gif]]></string>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/doc/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/doc/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/lib]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/lib]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples/groovy]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples/groovy]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/home/cruisecontrol/jalview/examples]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/examples]]></string>
</property>
<property name="shouldUninstall">
<boolean>false</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<boolean>false</boolean>
</property>
<property name="sourcePath">
- <string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/]]></string>
</property>
<property name="shouldUninstall">
<boolean>true</boolean>
<string><![CDATA[]]></string>
</property>
<property name="imagePath">
- <string><![CDATA[/home/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
+ <string><![CDATA[/homes/cruisecontrol/jalview/utils/InstallAnywhere/]]></string>
</property>
<property name="imageName">
<string><![CDATA[bartonGroup.gif]]></string>
<project name="jalviewInstallAnywhere" default="build" basedir=".">
<property name="IA_LOCATION" value="/home/cruisecontrol/InstallAnywhere 2013/"/>
<property name="IA_PROJECT" location="Jalview.iap_xml"/>
- <property name="ABS_PATH" value="/home/cruisecontrol/jalview"/> <!-- \/utils\/InstallAnywhere"/> --> <!--/home/cruisecontrol/jalview"/> -->
+ <property name="ABS_PATH" value="/homes/cruisecontrol/jalview"/> <!-- \/utils\/InstallAnywhere"/> --> <!--/home/cruisecontrol/jalview"/> -->
<!-- location of top level of jalview distribution directory -->
<property name="CUR_PATH" location="../../." />
<property name="USER_HOME" location="~" />
git://source.jalview.org / jalview.git / commitdiff