From: Jim Procter Date: Wed, 9 May 2018 09:39:51 +0000 (+0100) Subject: Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch X-Git-Tag: Release_2_10_4~5 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=32d1b850ae63a01a6b3fae305d9577ac16552515;hp=0b8133635dc649fb7710b9390a718c8f27a7f276;p=jalview.git Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch --- diff --git a/help/help.jhm b/help/help.jhm index f129193..d9a201a 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -54,6 +54,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 20dd8db..b218b88 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -24,6 +24,8 @@ + + diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index 68ac465..e1227de 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -211,41 +211,32 @@ structure in the alignment. The regions used to calculate the superposition will be highlighted using the 'Cartoon' rendering style, and the remaining data shown as a chain - trace.

+ trace.
+
-
  • EXPERIMENTAL FEATURES
    - - These are only available if the Tools→Enable - Experimental Features option is enabled. (Since Jalview 2.10.2) -
      -
    • Write Jalview features
      Selecting - this option will create new residue attributes for any - features currently visible in the associated alignment - views, allowing those positions to be selected and - analysed with via Chimera's 'Render by Attribute' tool - (found in the Tools submenu called Structure Analysis).
      -
      If you use this option, please remember to select - the Refresh Menus option in Chimera's Render by - Attribute dialog box in order to see the attributes - derived from Jalview sequence features. -
      - View - this function's issue in Jalview's bug tracker
      • -
    • Fetch Chimera Attributes
      This - submenu lists available Chimera residue attributes that - can be imported as Jalview features on associated - sequences.
      This is particularly useful for - transferring quantitative positional annotation. For - example, structure similarity for an alignment can be - visualised by transferring the local RMSD attributes - generated by Chimera's Match->Align tool onto aligned - sequences and displayed with a Graduated feature colour - scheme. -       View - this function's issue in Jalview's bug tracker
      • -
    • -
  • Help
    +
  • Write Jalview + features
    Selecting this option will create + new residue attributes for any features currently visible in + the associated alignment views, allowing those positions to + be selected and analysed with via Chimera's 'Render by + Attribute' tool (found in the Tools submenu called Structure + Analysis).

    If you use this option, please + remember to select the Refresh Menus option in + Chimera's Render by Attribute dialog box in order to see the + attributes derived from Jalview sequence features. +
    • +
  • Fetch Chimera Attributes
    This + submenu lists available Chimera residue attributes that can + be imported as Jalview features on associated sequences.
    This + is particularly useful for transferring quantitative + positional annotation. For example, structure similarity for + an alignment can be visualised by transferring the local + RMSD attributes generated by Chimera's Match->Align tool + onto aligned sequences and displayed with a Graduated feature colour + scheme.
    • + +
  • Help
    • Chimera Help
      diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index a93ce4b..d716e33 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -86,7 +86,7 @@ the Groovy Console for interactive scripting.
      • -
    • Enable Experimental Features Enable or disable features still under development in Jalview's user interface. This setting is remembered in your preferences. +
  • Vamsas For more details, read the diff --git a/help/html/releases.html b/help/html/releases.html index 528d635..63370bc 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -70,16 +70,16 @@ li:before {
    - 2.10.4
    1/05/2018     + 2.10.4
    8/05/2018
    • - Structure Chooser controls to - control superposition of multiple structures and open - structures in existing views + New Structure Chooser control + for disabling automatic superposition of multiple + structures and open structures in existing views
    • Mouse cursor changes to indicate Sequence @@ -96,7 +96,7 @@ li:before {
    • Improved performance when rendering lots - of features + of features (particularly when transparency is disabled)
    @@ -112,6 +112,19 @@ li:before { overlapping alignment panel
  • + overview doesn't show end of unpadded + sequence as gaps +
    • +
  • + Cross-reference handling improved: CDS not handled correctly if transcript has no UTR +
    • +
  • + Secondary structure and temperature + factor annotation not added to sequence when local PDB + file associated with it by drag'n'drop or structure + chooser +
    • +
  • Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views
    • @@ -146,19 +159,25 @@ li:before { as generated by CONSURF)
  • + Invert displayed features very slow when + structure and/or overview windows are also shown +
    • +
  • Selecting columns from highlighted regions very slow for alignments with large numbers of sequences
    • -
  • Copy Consensus fails for group consensus with 'StringIndexOutOfBounds'
    • -
  • New Defects -
      -
    • - 'SIFTS Mapping Error' when viewing - structures for protein subsequence (if 'Trim Retrieved - Sequences' enabled) or Ensembl isoforms (Workaround in - 2.10.4 is to fail back to N&W mapping) -
      • -
    +
  • + Copy Consensus fails for group consensus + with 'StringIndexOutOfBounds' +
    • +
  • + VAqua(4) provided as fallback Look and Feel for OSX + platforms running Java 10 +
    • +
  • + Adding a structure to existing structure + view appears to do nothing because the view is hidden behind the alignment view +
    • Applet
      @@ -166,7 +185,12 @@ li:before { Copy consensus sequence option in applet should copy the group consensus when popup is opened on it - +
    + Batch Mode +
      +
    • + Fixed ID width preference is not respected +
    New Known Defects
      @@ -179,6 +203,12 @@ li:before { repeatedly after a series of edits even when the overview is no longer reflecting updates +
    • + 'SIFTS Mapping Error' when viewing + structures for protein subsequence (if 'Trim Retrieved + Sequences' enabled) or Ensembl isoforms (Workaround in + 2.10.4 is to fail back to N&W mapping) +
    diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index d3972f5..0abd2a7 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -27,27 +27,24 @@ What's new in Jalview 2.10.4 ?

    - This is the February 2018 release of Jalview, with several minor bug fixes and enhanvements. - The full list bugs fixed in this release can be found in the 2.10.4 - Release Notes. In addition, Jalview 2.10.4 provides: + This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:

      -
    • +
    • Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
      • +
    • Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
      • +
    • Critical patches for running Jalview on OSX with Java 10
      • +
    • Easier adjustment of the Alignment ID panel and Annotation panel
      • +
    • Improved support for mapping between 3D Structures and Uniprot Protein Sequences
      • +
    • Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
      • +
    • New buttons on the Structure Chooser for adding structures + to an existing view, and disabling automatic superposition + according to linked alignments
      • +
    • Annotation transfer between Chimera and Jalview (formerly only + available in 'Experimental' mode)

    - Experimental Features + The full list of bugs fixed in this release can be found in the 2.10.4 + Release Notes.

    -

    - Remember, please enable the Experimental Features option in - the Jalview Desktop's Tools menu, and then restart Jalview - if you want to try out features below: -

    - - diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java index 2cd9348..8f778f7 100644 --- a/src/jalview/api/structures/JalviewStructureDisplayI.java +++ b/src/jalview/api/structures/JalviewStructureDisplayI.java @@ -120,4 +120,9 @@ public interface JalviewStructureDisplayI */ void setAlignAddedStructures(boolean alignAdded); + /** + * Raise the panel to the top of the stack... + */ + void raiseViewer(); + } diff --git a/src/jalview/datamodel/HiddenCursorPosition.java b/src/jalview/datamodel/HiddenCursorPosition.java index 160ed71..bdca6d0 100644 --- a/src/jalview/datamodel/HiddenCursorPosition.java +++ b/src/jalview/datamodel/HiddenCursorPosition.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; public final class HiddenCursorPosition diff --git a/src/jalview/datamodel/RangeElementsIterator.java b/src/jalview/datamodel/RangeElementsIterator.java index 85272f2..9ca6b2a 100644 --- a/src/jalview/datamodel/RangeElementsIterator.java +++ b/src/jalview/datamodel/RangeElementsIterator.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; import java.util.Iterator; diff --git a/src/jalview/datamodel/RangeIterator.java b/src/jalview/datamodel/RangeIterator.java index 7a69ac6..5d45236 100644 --- a/src/jalview/datamodel/RangeIterator.java +++ b/src/jalview/datamodel/RangeIterator.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; import java.util.ArrayList; diff --git a/src/jalview/datamodel/StartRegionIterator.java b/src/jalview/datamodel/StartRegionIterator.java index bd036e4..c21f04a 100644 --- a/src/jalview/datamodel/StartRegionIterator.java +++ b/src/jalview/datamodel/StartRegionIterator.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; import java.util.ArrayList; diff --git a/src/jalview/datamodel/VisibleContigsIterator.java b/src/jalview/datamodel/VisibleContigsIterator.java index 6d3f43d..0185978 100644 --- a/src/jalview/datamodel/VisibleContigsIterator.java +++ b/src/jalview/datamodel/VisibleContigsIterator.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; import java.util.ArrayList; diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 302ac3a..8832278 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -52,8 +52,6 @@ import java.util.List; import java.util.Map; import java.util.Vector; -import javax.swing.SwingUtilities; - import org.jmol.adapter.smarter.SmarterJmolAdapter; import org.jmol.api.JmolAppConsoleInterface; import org.jmol.api.JmolSelectionListener; @@ -480,6 +478,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel lastCommand = command; } + Thread colourby = null; /** * Sends a set of colour commands to the structure viewer * @@ -489,7 +488,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel protected void colourBySequence( final StructureMappingcommandSet[] colourBySequenceCommands) { - SwingUtilities.invokeLater(new Runnable() + if (colourby != null) + { + colourby.interrupt(); + colourby = null; + } + colourby = new Thread(new Runnable() { @Override public void run() @@ -503,6 +507,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } } }); + colourby.start(); } /** diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index dc3d0ee..2a510a2 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -28,7 +28,6 @@ import jalview.io.DataSourceType; import jalview.io.FileParse; import jalview.io.StructureFile; import jalview.schemes.ResidueProperties; -import jalview.structure.StructureImportSettings; import jalview.util.Format; import jalview.util.MessageManager; @@ -60,6 +59,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener { 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 { @@ -183,7 +188,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener } lastID = tmpatom.resNumIns.trim(); } - xferSettings(); + if (isParseImmediately()) + { + // configure parsing settings from the static singleton + xferSettings(); + } makeResidueList(); makeCaBondList(); @@ -200,7 +209,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener prot.add(chainseq); } - if (StructureImportSettings.isProcessSecondaryStructure()) + // look at local setting for adding secondary tructure + if (predictSecondaryStructure) { createAnnotation(chainseq, chain, ms.at); } diff --git a/src/jalview/fts/core/FTSRestClient.java b/src/jalview/fts/core/FTSRestClient.java index 076e212..f94d455 100644 --- a/src/jalview/fts/core/FTSRestClient.java +++ b/src/jalview/fts/core/FTSRestClient.java @@ -284,7 +284,8 @@ public abstract class FTSRestClient implements FTSRestClientI public boolean equals(Object otherObject) { FTSDataColumnI that = (FTSDataColumnI) otherObject; - return this.getCode().equals(that.getCode()) + return otherObject == null ? false + : this.getCode().equals(that.getCode()) && this.getName().equals(that.getName()) && this.getGroup().equals(that.getGroup()); } diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 6342cf0..d07a7c2 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -100,41 +100,34 @@ public class ChimeraViewFrame extends StructureViewerBase savemenu.setVisible(false); // not yet implemented viewMenu.add(fitToWindow); - /* - * exchange of Jalview features and Chimera attributes is for now - * an optionally enabled experimental feature - */ - if (Desktop.instance.showExperimental()) + JMenuItem writeFeatures = new JMenuItem( + MessageManager.getString("label.create_chimera_attributes")); + writeFeatures.setToolTipText(MessageManager + .getString("label.create_chimera_attributes_tip")); + writeFeatures.addActionListener(new ActionListener() { - JMenuItem writeFeatures = new JMenuItem( - MessageManager.getString("label.create_chimera_attributes")); - writeFeatures.setToolTipText(MessageManager - .getString("label.create_chimera_attributes_tip")); - writeFeatures.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - sendFeaturesToChimera(); - } - }); - viewerActionMenu.add(writeFeatures); - - final JMenu fetchAttributes = new JMenu( - MessageManager.getString("label.fetch_chimera_attributes")); - fetchAttributes.setToolTipText(MessageManager - .getString("label.fetch_chimera_attributes_tip")); - fetchAttributes.addMouseListener(new MouseAdapter() + @Override + public void actionPerformed(ActionEvent e) { + sendFeaturesToChimera(); + } + }); + viewerActionMenu.add(writeFeatures); - @Override - public void mouseEntered(MouseEvent e) - { - buildAttributesMenu(fetchAttributes); - } - }); - viewerActionMenu.add(fetchAttributes); - } + final JMenu fetchAttributes = new JMenu( + MessageManager.getString("label.fetch_chimera_attributes")); + fetchAttributes.setToolTipText( + MessageManager.getString("label.fetch_chimera_attributes_tip")); + fetchAttributes.addMouseListener(new MouseAdapter() + { + + @Override + public void mouseEntered(MouseEvent e) + { + buildAttributesMenu(fetchAttributes); + } + }); + viewerActionMenu.add(fetchAttributes); } /** diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java index 35a4bc6..0c8354b 100644 --- a/src/jalview/gui/StructureViewer.java +++ b/src/jalview/gui/StructureViewer.java @@ -293,6 +293,7 @@ public class StructureViewer sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId); } sview.updateTitleAndMenus(); + sview.raiseViewer(); return sview; } ViewerType viewerType = getViewerType(); diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index 840dbae..72b0bcc 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -1034,4 +1034,10 @@ public abstract class StructureViewerBase extends GStructureViewer return seqColoursApplied; } + @Override + public void raiseViewer() + { + toFront(); + } + } diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 2340283..497f0a5 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -72,7 +72,20 @@ public abstract class AlignFile extends FileParse 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. @@ -153,6 +166,11 @@ public abstract class AlignFile extends FileParse { 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(); diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java index a30be66..240e1fd 100644 --- a/src/jalview/jbgui/GStructureChooser.java +++ b/src/jalview/jbgui/GStructureChooser.java @@ -1,6 +1,6 @@ /* - * 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. * diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index ad259fd..cd986c0 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -398,8 +398,11 @@ public class StructureSelectionManager { // 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) { diff --git a/test/jalview/gui/SeqCanvasTest.java b/test/jalview/gui/SeqCanvasTest.java index fb48fdb..ee1270e 100644 --- a/test/jalview/gui/SeqCanvasTest.java +++ b/test/jalview/gui/SeqCanvasTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.gui; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java index bc9c2e4..1d532f7 100644 --- a/test/jalview/renderer/OverviewRendererTest.java +++ b/test/jalview/renderer/OverviewRendererTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.renderer; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java index 3d48097..6bb611c 100644 --- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java +++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.renderer.seqfeatures; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java index 85aea40..4bee3f5 100644 --- a/test/jalview/structure/Mapping.java +++ b/test/jalview/structure/Mapping.java @@ -260,6 +260,8 @@ public class Mapping @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", diff --git a/test/jalview/structure/StructureMappingTest.java b/test/jalview/structure/StructureMappingTest.java index 036aeaa..808e662 100644 --- a/test/jalview/structure/StructureMappingTest.java +++ b/test/jalview/structure/StructureMappingTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.structure; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/ws/dbsources/PfamFullTest.java b/test/jalview/ws/dbsources/PfamFullTest.java index b914a45..f5cc640 100644 --- a/test/jalview/ws/dbsources/PfamFullTest.java +++ b/test/jalview/ws/dbsources/PfamFullTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.dbsources; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/ws/dbsources/PfamSeedTest.java b/test/jalview/ws/dbsources/PfamSeedTest.java index 2fa1871..355ef0c 100644 --- a/test/jalview/ws/dbsources/PfamSeedTest.java +++ b/test/jalview/ws/dbsources/PfamSeedTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.dbsources; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/ws/dbsources/RfamFullTest.java b/test/jalview/ws/dbsources/RfamFullTest.java index cb60b14..2d1497f 100644 --- a/test/jalview/ws/dbsources/RfamFullTest.java +++ b/test/jalview/ws/dbsources/RfamFullTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.dbsources; import static org.testng.Assert.assertEquals; diff --git a/test/jalview/ws/dbsources/RfamSeedTest.java b/test/jalview/ws/dbsources/RfamSeedTest.java index 5ca72c2..745ba2e 100644 --- a/test/jalview/ws/dbsources/RfamSeedTest.java +++ b/test/jalview/ws/dbsources/RfamSeedTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.dbsources; import static org.testng.Assert.assertEquals; diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml index d4541f1..20726f5 100755 --- a/utils/InstallAnywhere/Jalview.iap_xml +++ b/utils/InstallAnywhere/Jalview.iap_xml @@ -2337,7 +2337,7 @@ and any path to a file to save to the file]]> - + false @@ -2355,7 +2355,7 @@ and any path to a file to save to the file]]> true - + 1355141