X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=e01d40acb22462298ea342dd0798e893bb8ad460;hb=b2d2f19d703fe5c499788bbd2947e65ac1ca7441;hp=faa5e4390ce214d4821560d72b63450757038aad;hpb=028dbea7b4d76fb62d77d52879c37316eaca5d93;p=jalview.git
diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index faa5e43..e01d40a 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -1,9 +1,28 @@
+/*
+ * 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.bin;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
-import java.lang.reflect.Field;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.Arrays;
@@ -14,6 +33,8 @@ import java.util.List;
import java.util.Locale;
import java.util.Map;
+import javax.swing.SwingUtilities;
+
import jalview.analysis.AlignmentUtils;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Jalview.ExitCode;
@@ -25,8 +46,6 @@ import jalview.bin.argparser.SubVals;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
-import jalview.ext.jmol.JalviewJmolBinding;
-import jalview.ext.jmol.JmolCommands;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
import jalview.gui.AppJmol;
@@ -51,7 +70,6 @@ import jalview.io.exceptions.ImageOutputException;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureCommandI;
-import jalview.structure.StructureCommandsI;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
@@ -198,7 +216,7 @@ public class Commands
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
- long progress = -1;
+ final long progress = System.currentTimeMillis();
boolean first = true;
boolean progressBarSet = false;
@@ -224,10 +242,18 @@ public class Commands
first = false;
if (!headless && desktop != null)
{
- desktop.setProgressBar(
- MessageManager.getString(
- "status.processing_commandline_args"),
- progress = System.currentTimeMillis());
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ desktop.setProgressBar(
+ MessageManager.getString(
+ "status.processing_commandline_args"),
+ progress);
+
+ }
+ });
progressBarSet = true;
}
}
@@ -369,24 +395,49 @@ public class Commands
boolean showSSAnnotations = avm.getFromSubValArgOrPref(
Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
- af.setAnnotationsVisibility(showSSAnnotations, true, false);
// Show sequence annotations?
boolean showAnnotations = avm.getFromSubValArgOrPref(
Arg.SHOWANNOTATIONS, av.getSubVals(), null,
"SHOW_ANNOTATIONS", true);
- af.setAnnotationsVisibility(showAnnotations, false, true);
- // show temperature factor annotations?
- if (avm.getBoolean(Arg.NOTEMPFAC))
+ boolean hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
+ final AlignFrame _af = af;
+ // many of jalview's format/layout methods are only thread safe on the
+ // swingworker thread.
+ // all these methods should be on the alignViewController so it can
+ // coordinate such details
+ try
{
- // do this better (annotation types?)
- List hideThese = new ArrayList<>();
- hideThese.add("Temperature Factor");
- hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(), hideThese, null,
- false, false);
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ _af.setAnnotationsVisibility(showSSAnnotations, true,
+ false);
+
+ _af.setAnnotationsVisibility(showAnnotations, false, true);
+
+ // show temperature factor annotations?
+ if (hideTFrows)
+ {
+ // do this better (annotation types?)
+ List hideThese = new ArrayList<>();
+ hideThese.add("Temperature Factor");
+ hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ _af.getCurrentView().getAlignment(), hideThese,
+ null, false, false);
+ }
+ }
+ });
+ } catch (Exception x)
+ {
+ Console.warn(
+ "Unexpected exception adjusting annotation row visibility.",
+ x);
}
// wrap alignment? do this last for formatting reasons
@@ -412,9 +463,11 @@ public class Commands
{
Console.debug(
"Opening '" + openFile + "' in existing alignment frame");
+
DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
? DataSourceType.URL
: DataSourceType.FILE;
+
FileLoader fileLoader = new FileLoader(!headless);
fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
false);
@@ -443,17 +496,18 @@ public class Commands
// open the structure (from same PDB file or given PDBfile)
if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
+
AlignFrame af = afMap.get(id);
if (avm.containsArg(Arg.STRUCTURE))
{
commandArgsProvided = true;
- for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
+ for (ArgValue structureAv : avm.getArgValueList(Arg.STRUCTURE))
{
argParser.setStructureFilename(null);
- String val = av.getValue();
- SubVals subVals = av.getSubVals();
- int argIndex = av.getArgIndex();
- SequenceI seq = getSpecifiedSequence(af, avm, av);
+ String val = structureAv.getValue();
+ SubVals subVals = structureAv.getSubVals();
+ int argIndex = structureAv.getArgIndex();
+ SequenceI seq = getSpecifiedSequence(af, avm, structureAv);
if (seq == null)
{
// Could not find sequence from subId, let's assume the first
@@ -522,8 +576,8 @@ public class Commands
// get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
String paeFilepath = avm.getFromSubValArgOrPrefWithSubstitutions(
- argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER, av,
- subVals, null, null, null);
+ argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER,
+ structureAv, subVals, null, null, null);
if (paeFilepath != null)
{
File paeFile = new File(paeFilepath);
@@ -547,8 +601,8 @@ public class Commands
// get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
// reference annotations
String tftString = avm.getFromSubValArgOrPrefWithSubstitutions(
- argParser, Arg.TEMPFAC, ArgValuesMap.Position.AFTER, av,
- subVals, null, null, null);
+ argParser, Arg.TEMPFAC, ArgValuesMap.Position.AFTER,
+ structureAv, subVals, null, null, null);
boolean notempfac = avm.getFromSubValArgOrPref(Arg.NOTEMPFAC,
subVals, null, "ADD_TEMPFACT_ANN", false, true);
TFType tft = notempfac ? null : TFType.DEFAULT;
@@ -580,8 +634,8 @@ public class Commands
}
String sViewerName = avm.getFromSubValArgOrPref(
- Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER, av,
- subVals, null, null, "jmol");
+ Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER,
+ structureAv, subVals, null, null, "jmol");
ViewerType viewerType = ViewerType.getFromString(sViewerName);
// TODO use ssFromStructure
@@ -642,7 +696,8 @@ public class Commands
if (avm.containsArg(Arg.STRUCTUREIMAGE))
{
for (ArgValue structureImageArgValue : avm
- .getArgValueList(Arg.STRUCTUREIMAGE))
+ .getArgValueListFromSubValOrArg(structureAv,
+ Arg.STRUCTUREIMAGE, subVals))
{
String structureImageFilename = argParser.makeSubstitutions(
structureImageArgValue.getValue(), id, true);
@@ -686,7 +741,8 @@ public class Commands
/////
// DON'T TRY TO EXPORT IF VIEWER IS UNSUPPORTED
- if (viewerType!=ViewerType.JMOL) {
+ if (viewerType != ViewerType.JMOL)
+ {
addWarn("Cannot export image for structure viewer "
+ viewerType.name() + " yet");
continue;
@@ -695,7 +751,7 @@ public class Commands
/////
// Apply the temporary colourscheme to the linked alignment
// TODO: enhance for multiple linked alignments.
-
+
String imageColour = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.IMAGECOLOUR,
structureImageSubVals);
@@ -712,27 +768,12 @@ public class Commands
Color bgcolour = null;
if (bgcolourstring != null && bgcolourstring.length() > 0)
{
- try
- {
- //
- // FIXME: Why not use ColorUtils.parseColourString(bgcolourstring) - this is consistent and backwards compatible
- //
- if (bgcolourstring.charAt(0) == '#')
- {
- bgcolour = Color.decode(bgcolourstring);
- }
- else
- {
- Field field = Color.class.getField(bgcolourstring);
- bgcolour = (Color) field.get(null);
- }
- } catch (IllegalArgumentException | NoSuchFieldException
- | SecurityException | IllegalAccessException nfe)
+ bgcolour = ColorUtils.parseColourString(bgcolourstring);
+ if (bgcolour == null)
{
Console.warn(
"Background colour string '" + bgcolourstring
+ "' not recognised -- using default");
- //bgcolour = Color.black;
}
}
@@ -740,72 +781,82 @@ public class Commands
.getJalviewStructureDisplay();
File sessionToRestore = null;
-
- List extraCommands=new ArrayList<>();
-
- if (extraCommands.size() > 0 || bgcolour!=null)
+
+ List extraCommands = new ArrayList<>();
+
+ if (extraCommands.size() > 0 || bgcolour != null)
{
- try {
+ try
+ {
sessionToRestore = sview.saveSession();
} catch (Throwable t)
{
- Console.warn("Unable to save temporary session file before custom structure view export operation.");
+ Console.warn(
+ "Unable to save temporary session file before custom structure view export operation.");
}
}
-
+
////
- // Do temporary ops
+ // Do temporary ops
+
+ if (bgcolour != null)
+ {
+ sview.getBinding().setBackgroundColour(bgcolour);
+ }
+
+ sview.getBinding().executeCommands(extraCommands, false,
+ "Executing Custom Commands");
- sview.getBinding().setBackgroundColour(bgcolour);
-
- sview.getBinding().executeCommands(extraCommands, false, "Executing Custom Commands");
-
// and export the view as an image
boolean success = this.checksBeforeWritingToFile(avm,
subVals, false, structureImageFilename,
"structure image", isError);
-
+
if (!success)
{
continue;
}
- Console.debug(
- "Rendering image to " + structureImageFile);
- //
- // TODO - extend StructureViewer / Binding with makePDBImage so we can do this with every viewer
- //
-
- try {
+ Console.debug("Rendering image to " + structureImageFile);
+ //
+ // TODO - extend StructureViewer / Binding with makePDBImage so
+ // we can do this with every viewer
+ //
+
+ try
+ {
// We don't expect class cast exception
AppJmol jmol = (AppJmol) sview;
- jmol.makePDBImage(structureImageFile, imageType,
- renderer, userBis);
- Console.debug("Finished Rendering image to "
+ jmol.makePDBImage(structureImageFile, imageType, renderer,
+ userBis);
+ Console.info("Exported structure image to "
+ structureImageFile);
-
+
// RESTORE SESSION AFTER EXPORT IF NEED BE
if (sessionToRestore != null)
{
- Console.debug("Restoring session from "
- + sessionToRestore);
-
- sview.getBinding().restoreSession(sessionToRestore.getAbsolutePath());
+ Console.debug(
+ "Restoring session from " + sessionToRestore);
+
+ sview.getBinding().restoreSession(
+ sessionToRestore.getAbsolutePath());
}
- } catch (ImageOutputException ioexc)
+ } catch (ImageOutputException ioexec)
{
- addError("Unexpected error whilst exporting image to "
- + structureImageFile, ioexc);
+ addError(
+ "Unexpected error when restoring structure viewer session after custom view operations.");
isError = true;
continue;
- }
- finally
+ } finally
{
- try {
+ try
+ {
this.colourAlignFrame(af, originalColourScheme);
} catch (Exception t)
{
- addError("Unexpected error when restoring colourscheme to alignment after temporary change for export.",t);
+ addError(
+ "Unexpected error when restoring colourscheme to alignment after temporary change for export.",
+ t);
}
}
}
@@ -818,6 +869,7 @@ public class Commands
if (wrap)
{
+
AlignFrame af = afMap.get(id);
if (af != null)
{
@@ -829,16 +881,16 @@ public class Commands
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
{
- AlignFrame af = afMap.get(id);
- for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
- .findAnnotation(PDBChain.class.getName().toString()))
- {
- AnnotationColourGradient acg = new AnnotationColourGradient(aa,
- af.alignPanel.av.getGlobalColourScheme(), 0);
- acg.setSeqAssociated(true);
- af.changeColour(acg);
- Console.info("Changed colour " + acg.toString());
- }
+ AlignFrame af = afMap.get(id);
+ for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+ .findAnnotation(PDBChain.class.getName().toString()))
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+ af.alignPanel.av.getGlobalColourScheme(), 0);
+ acg.setSeqAssociated(true);
+ af.changeColour(acg);
+ Console.info("Changed colour " + acg.toString());
+ }
}
*/
@@ -850,21 +902,29 @@ public class Commands
ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
- if (af == null)
+ if (avm != null && !avm.containsArg(Arg.GROOVY))
{
- addWarn("Did not have an alignment window for id=" + id);
+ // nothing to do
return;
}
+ if (af == null)
+ {
+ addWarn("Groovy script does not have an alignment window. Proceeding with caution!");
+ }
+
if (avm.containsArg(Arg.GROOVY))
{
- String groovyscript = avm.getValue(Arg.GROOVY);
- if (groovyscript != null)
+ for (ArgValue groovyAv : avm.getArgValueList(Arg.GROOVY))
{
- // Execute the groovy script after we've done all the rendering stuff
- // and before any images or figures are generated.
- Console.info("Executing script " + groovyscript);
- Jalview.getInstance().executeGroovyScript(groovyscript, af);
+ String groovyscript = groovyAv.getValue();
+ if (groovyscript != null)
+ {
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ Console.info("Executing script " + groovyscript);
+ Jalview.getInstance().executeGroovyScript(groovyscript, af);
+ }
}
}
}
@@ -874,9 +934,16 @@ public class Commands
ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
+ if (avm != null && !avm.containsArg(Arg.IMAGE))
+ {
+ // nothing to do
+ return true;
+ }
+
if (af == null)
{
- addWarn("Did not have an alignment window for id=" + id);
+ addWarn("Do not have an alignment window to create image from (id="
+ + id + "). Not proceeding.");
return false;
}
@@ -1003,9 +1070,16 @@ public class Commands
ArgValuesMap avm = argParser.getLinkedArgs(id);
AlignFrame af = afMap.get(id);
+ if (avm != null && !avm.containsArg(Arg.OUTPUT))
+ {
+ // nothing to do
+ return true;
+ }
+
if (af == null)
{
- addWarn("Did not have an alignment window for id=" + id);
+ addWarn("Do not have an alignment window (id=" + id
+ + "). Not proceeding.");
return false;
}