From: tcofoegbu Date: Thu, 3 Sep 2015 16:07:42 +0000 (+0100) Subject: merge X-Git-Tag: Release_2_10_0~475^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeatures%2FJAL-857_dynamic-example-files;hp=0f427c676c3380fd8fe1856c9eff8b653f3e4815;p=jalview.git merge --- diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index f60bb6a..850b223 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -430,6 +430,7 @@ + diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java index cb19769..ddfa1b0 100644 --- a/src/jalview/ext/jmol/PDBFileWithJmol.java +++ b/src/jalview/ext/jmol/PDBFileWithJmol.java @@ -45,7 +45,6 @@ import org.jmol.modelset.ModelSet; import org.jmol.modelsetbio.BioModel; import org.jmol.modelsetbio.BioPolymer; import org.jmol.viewer.Viewer; -import org.openscience.jmol.app.JmolApp; /** * Import and process PDB files with Jmol @@ -56,9 +55,6 @@ import org.openscience.jmol.app.JmolApp; public class PDBFileWithJmol extends AlignFile implements JmolStatusListener { - - JmolApp jmolApp = null; - Viewer viewer = null; public PDBFileWithJmol(String inFile, String type) throws IOException @@ -73,7 +69,6 @@ public class PDBFileWithJmol extends AlignFile implements public PDBFileWithJmol() { - // TODO Auto-generated constructor stub } /** @@ -84,18 +79,11 @@ public class PDBFileWithJmol extends AlignFile implements private Viewer getJmolData() { if (viewer == null) - { // note that -o -n -x are all implied // TODO check for Jmol 14.2 - jmolApp = new JmolApp(); - jmolApp.isDataOnly = true; - jmolApp.haveConsole = false; - jmolApp.haveDisplay = false; + { try { viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null, null, "-x -o -n", this); - viewer.setScreenDimension(jmolApp.startupWidth, - jmolApp.startupHeight); - jmolApp.startViewer(viewer, null, false); } catch (ClassCastException x) { throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}), diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 39aa257..2a360cc 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -3065,15 +3065,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements } - // public static AlignFrame getCurrentAlignFrame() - // { - // return currentAlignFrame; - // } - // - // public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) - // { - // Desktop.currentAlignFrame = currentAlignFrame; - // } + public static AlignFrame getCurrentAlignFrame() + { + return currentAlignFrame; + } + + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + Desktop.currentAlignFrame = currentAlignFrame; + } } diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 23b09de..2f90e91 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.ViewStyleI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignedCodonFrame; @@ -1149,6 +1150,7 @@ public class Jalview2XML view.setFontName(av.font.getName()); view.setFontSize(av.font.getSize()); view.setFontStyle(av.font.getStyle()); + view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna()); view.setRenderGaps(av.isRenderGaps()); view.setShowAnnotation(av.isShowAnnotation()); view.setShowBoxes(av.getShowBoxes()); @@ -4194,6 +4196,9 @@ public class Jalview2XML af.viewport.setFont( new java.awt.Font(view.getFontName(), view.getFontStyle(), view .getFontSize()), true); + ViewStyleI vs = af.viewport.getViewStyle(); + vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna()); + af.viewport.setViewStyle(vs); // TODO: allow custom charWidth/Heights to be restored by updating them // after setting font - which means set above to false af.viewport.setRenderGaps(view.getRenderGaps()); diff --git a/src/jalview/gui/PDBSearchPanel.java b/src/jalview/gui/PDBSearchPanel.java index b31c637..4e23f57 100644 --- a/src/jalview/gui/PDBSearchPanel.java +++ b/src/jalview/gui/PDBSearchPanel.java @@ -195,6 +195,7 @@ public class PDBSearchPanel extends GPDBSearchPanel public void loadSelectedPDBSequencesToAlignment() { // mainFrame.dispose(); + disableActionButtons(); StringBuilder selectedIds = new StringBuilder(); HashSet selectedIdsSet = new HashSet(); int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false); @@ -217,6 +218,35 @@ public class PDBSearchPanel extends GPDBSearchPanel seqFetcher.textArea.setText(ids); Thread worker = new Thread(seqFetcher); worker.start(); + delayAndEnableActionButtons(); + + } + + private void disableActionButtons() + { + btn_ok.setEnabled(false); + btn_back.setEnabled(false); + btn_cancel.setEnabled(false); + } + + private void delayAndEnableActionButtons() + { + new Thread() + { + public void run() + { + try + { + Thread.sleep(1500); + } catch (InterruptedException e) + { + e.printStackTrace(); + } + btn_ok.setEnabled(true); + btn_back.setEnabled(true); + btn_cancel.setEnabled(true); + } + }.start(); } public static String getPDBIdwithSpecifiedChain(String pdbId, diff --git a/src/jalview/json/binding/biojson/v1/JalviewBioJsColorSchemeMapper.java b/src/jalview/json/binding/biojson/v1/JalviewBioJsColorSchemeMapper.java index 094adad..92184ea 100644 --- a/src/jalview/json/binding/biojson/v1/JalviewBioJsColorSchemeMapper.java +++ b/src/jalview/json/binding/biojson/v1/JalviewBioJsColorSchemeMapper.java @@ -22,7 +22,7 @@ public enum JalviewBioJsColorSchemeMapper "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor", new TaylorColourScheme()), NUCLEOTIDE("Nucleotide", "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE( - "Purine/Pyrimidine", "purine", new PurinePyrimidineColourScheme()), HELIX_PROPENCITY( + "Purine/Pyrimidine", "purine", new PurinePyrimidineColourScheme()), HELIX_PROPENSITY( "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY( "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY( "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX( diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr index e01bbd4..361fb7c 100644 --- a/src/jalview/schemabinding/version2/.castor.cdr +++ b/src/jalview/schemabinding/version2/.castor.cdr @@ -1,4 +1,4 @@ -#Fri Jun 26 14:22:47 BST 2015 +#Thu Sep 03 10:55:37 BST 2015 jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 136a3b3..e3a19de 100644 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -332,6 +332,16 @@ public class Viewport implements java.io.Serializable { private boolean _has_fontStyle; /** + * Field _scaleProteinAsCdna. + */ + private boolean _scaleProteinAsCdna = true; + + /** + * keeps track of state for field: _scaleProteinAsCdna + */ + private boolean _has_scaleProteinAsCdna; + + /** * Field _viewName. */ private java.lang.String _viewName; @@ -631,6 +641,13 @@ public class Viewport implements java.io.Serializable { /** */ + public void deleteScaleProteinAsCdna( + ) { + this._has_scaleProteinAsCdna= false; + } + + /** + */ public void deleteShowAnnotation( ) { this._has_showAnnotation= false; @@ -1107,6 +1124,16 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'scaleProteinAsCdna'. + * + * @return the value of field 'ScaleProteinAsCdna'. + */ + public boolean getScaleProteinAsCdna( + ) { + return this._scaleProteinAsCdna; + } + + /** * Returns the value of field 'sequenceSetId'. * * @return the value of field 'SequenceSetId'. @@ -1510,6 +1537,16 @@ public class Viewport implements java.io.Serializable { } /** + * Method hasScaleProteinAsCdna. + * + * @return true if at least one ScaleProteinAsCdna has been adde + */ + public boolean hasScaleProteinAsCdna( + ) { + return this._has_scaleProteinAsCdna; + } + + /** * Method hasShowAnnotation. * * @return true if at least one ShowAnnotation has been added @@ -1834,6 +1871,16 @@ public class Viewport implements java.io.Serializable { } /** + * Returns the value of field 'scaleProteinAsCdna'. + * + * @return the value of field 'ScaleProteinAsCdna'. + */ + public boolean isScaleProteinAsCdna( + ) { + return this._scaleProteinAsCdna; + } + + /** * Returns the value of field 'showAnnotation'. * * @return the value of field 'ShowAnnotation'. @@ -2382,6 +2429,18 @@ public class Viewport implements java.io.Serializable { } /** + * Sets the value of field 'scaleProteinAsCdna'. + * + * @param scaleProteinAsCdna the value of field + * 'scaleProteinAsCdna'. + */ + public void setScaleProteinAsCdna( + final boolean scaleProteinAsCdna) { + this._scaleProteinAsCdna = scaleProteinAsCdna; + this._has_scaleProteinAsCdna = true; + } + + /** * Sets the value of field 'sequenceSetId'. * * @param sequenceSetId the value of field 'sequenceSetId'. diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java index 0044f5b..cea458c 100644 --- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java @@ -1375,6 +1375,47 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr typeValidator.setMaxInclusive(2147483647); } desc.setValidator(fieldValidator); + //-- _scaleProteinAsCdna + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleProteinAsCdna", "scaleProteinAsCdna", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasScaleProteinAsCdna()) { return null; } + return (target.getScaleProteinAsCdna() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScaleProteinAsCdna(); + return; + } + target.setScaleProteinAsCdna( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _scaleProteinAsCdna + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); //-- _viewName desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute); desc.setImmutable(true);