+/*
+ * 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.bin;
+import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.net.URISyntaxException;
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;
import jalview.io.exceptions.ImageOutputException;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.StructureCommandI;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
import jalview.util.FileUtils;
import jalview.util.HttpUtils;
import jalview.util.ImageMaker;
}
- // report errors
- Console.warn(
- "The following errors and warnings occurred whilst processing files:\n"
- + errorsToString());
+ // report errors - if any
+ String errorsRaised = errorsToString();
+ if (errorsRaised.trim().length() > 0)
+ {
+ Console.warn(
+ "The following errors and warnings occurred whilst processing files:\n"
+ + errorsRaised);
+ }
// gui errors reported in Jalview
if (argParser.getBoolean(Arg.QUIT))
Boolean isError = Boolean.valueOf(false);
- // set wrap scope here so it can be applied after structures are opened
+ // set wrap, showSSAnnotations, showAnnotations and hideTFrows scope here so
+ // it can be applied after structures are opened
boolean wrap = false;
+ boolean showSSAnnotations = false;
+ boolean showAnnotations = false;
+ boolean hideTFrows = false;
+ AlignFrame af = null;
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;
- AlignFrame af;
// Combine the APPEND and OPEN files into one list, along with whether it
// was APPEND or OPEN
List<ArgValue> openAvList = new ArrayList<>();
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;
}
}
}
// Show secondary structure annotations?
- boolean showSSAnnotations = avm.getFromSubValArgOrPref(
+ 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);
+ showAnnotations = avm.getFromSubValArgOrPref(Arg.SHOWANNOTATIONS,
+ av.getSubVals(), null, "SHOW_ANNOTATIONS", true);
+ // hide the Temperature Factor row?
+ hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
- // show temperature factor annotations?
- if (avm.getBoolean(Arg.NOTEMPFAC))
- {
- // do this better (annotation types?)
- List<String> hideThese = new ArrayList<>();
- hideThese.add("Temperature Factor");
- hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(), hideThese, null,
- false, false);
- }
+ // showSSAnnotations, showAnnotations, hideTFrows used after opening
+ // structure
// wrap alignment? do this last for formatting reasons
wrap = avm.getFromSubValArgOrPref(Arg.WRAP, sv, null,
{
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);
// open the structure (from same PDB file or given PDBfile)
if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
- AlignFrame af = afMap.get(id);
+ if (af == null)
+ {
+ 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))
{
- String val = av.getValue();
- SubVals subVals = av.getSubVals();
- int argIndex = av.getArgIndex();
- SequenceI seq = getSpecifiedSequence(af, avm, av);
+ argParser.setStructureFilename(null);
+ 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
// 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);
// 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;
}
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
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);
BitmapImageSizing userBis = ImageMaker
.parseScaleWidthHeightStrings(scale, width, height);
+ /////
+ // DON'T TRY TO EXPORT IF VIEWER IS UNSUPPORTED
+ if (viewerType != ViewerType.JMOL)
+ {
+ addWarn("Cannot export image for structure viewer "
+ + viewerType.name() + " yet");
+ continue;
+ }
+
+ /////
+ // Apply the temporary colourscheme to the linked alignment
+ // TODO: enhance for multiple linked alignments.
+
String imageColour = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.IMAGECOLOUR,
structureImageSubVals);
.getColourScheme(af);
this.colourAlignFrame(af, imageColour);
- List<String> extraCommands = new ArrayList<>();
- // these don't actually do anything to the output image since we
- // renderScreenImage
- // extraCommands.add("set antialiasImages on");
- // extraCommands.add("set antialiasTranslucent on");
+ /////
+ // custom image background colour
- String bgcolour = avm.getValueFromSubValOrArg(
+ String bgcolourstring = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.BGCOLOUR,
structureImageSubVals);
- if (bgcolour != null && bgcolour.length() > 0)
+ Color bgcolour = null;
+ if (bgcolourstring != null && bgcolourstring.length() > 0)
{
- if (bgcolour.charAt(0) == '#')
+ bgcolour = ColorUtils.parseColourString(bgcolourstring);
+ if (bgcolour == null)
{
- bgcolour = "[x" + bgcolour.substring(1) + "]";
+ Console.warn(
+ "Background colour string '" + bgcolourstring
+ + "' not recognised -- using default");
}
- extraCommands.add("background " + bgcolour);
}
- // TODO MAKE THIS VIEWER INDEPENDENT!!
- switch (StructureViewer.getViewerType())
+ JalviewStructureDisplayI sview = structureViewer
+ .getJalviewStructureDisplay();
+
+ File sessionToRestore = null;
+
+ List<StructureCommandI> extraCommands = new ArrayList<>();
+
+ if (extraCommands.size() > 0 || bgcolour != null)
+ {
+ try
+ {
+ sessionToRestore = sview.saveSession();
+ } catch (Throwable t)
+ {
+ Console.warn(
+ "Unable to save temporary session file before custom structure view export operation.");
+ }
+ }
+
+ ////
+ // Do temporary ops
+
+ if (bgcolour != null)
+ {
+ 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)
{
- case JMOL:
- JalviewStructureDisplayI sview = structureViewer
- .getJalviewStructureDisplay();
- if (sview instanceof AppJmol)
+ continue;
+ }
+ 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.info("Exported structure image to "
+ + structureImageFile);
+
+ // RESTORE SESSION AFTER EXPORT IF NEED BE
+ if (sessionToRestore != null)
{
- AppJmol jmol = (AppJmol) sview;
- try
- {
- boolean success = this.checksBeforeWritingToFile(avm,
- subVals, false, structureImageFilename,
- "structure image", isError);
- if (!success)
- {
- continue;
- }
-
- Console.debug(
- "Rendering image to " + structureImageFile);
- jmol.makePDBImage(structureImageFile, imageType,
- renderer, userBis, extraCommands);
- Console.debug("Finished Rendering image to "
- + structureImageFile);
-
- } catch (ImageOutputException ioexc)
- {
- addError("Unexpected error whilst exporting image to "
- + structureImageFile, ioexc);
- isError = true;
- continue;
- }
+ Console.debug(
+ "Restoring session from " + sessionToRestore);
+
+ sview.getBinding().restoreSession(
+ sessionToRestore.getAbsolutePath());
}
- break;
- default:
- addWarn("Cannot export image for structure viewer "
- + structureViewer.getViewerType() + " yet");
+ } catch (ImageOutputException ioexec)
+ {
+ addError(
+ "Unexpected error when restoring structure viewer session after custom view operations.");
+ isError = true;
continue;
+ } finally
+ {
+ try
+ {
+ this.colourAlignFrame(af, originalColourScheme);
+ } catch (Exception t)
+ {
+ addError(
+ "Unexpected error when restoring colourscheme to alignment after temporary change for export.",
+ t);
+ }
}
- this.colourAlignFrame(af, originalColourScheme);
}
}
}
+ argParser.setStructureFilename(null);
}
}
}
+ if (af == null)
+ {
+ af = afMap.get(id);
+ }
+ // 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
+ if (headless)
+ {
+ showOrHideAnnotations(af, showSSAnnotations, showAnnotations,
+ hideTFrows);
+ }
+ else
+ {
+ try
+ {
+ AlignFrame _af = af;
+ final boolean _showSSAnnotations = showSSAnnotations;
+ final boolean _showAnnotations = showAnnotations;
+ final boolean _hideTFrows = hideTFrows;
+ SwingUtilities.invokeAndWait(() -> {
+ showOrHideAnnotations(_af, _showSSAnnotations, _showAnnotations,
+ _hideTFrows);
+ }
+
+ );
+ } catch (Exception x)
+ {
+ Console.warn(
+ "Unexpected exception adjusting annotation row visibility.",
+ x);
+ }
+ }
+
if (wrap)
{
- AlignFrame af = afMap.get(id);
+ if (af == null)
+ {
+ af = afMap.get(id);
+ }
if (af != null)
{
af.setWrapFormat(wrap, true);
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());
+ }
}
*/
return theseArgsWereParsed && !isError;
}
+ private static void showOrHideAnnotations(AlignFrame af,
+ boolean showSSAnnotations, boolean showAnnotations,
+ boolean hideTFrows)
+ {
+ af.setAnnotationsVisibility(showSSAnnotations, true, false);
+ af.setAnnotationsVisibility(showAnnotations, false, true);
+
+ // show temperature factor annotations?
+ if (hideTFrows)
+ {
+ // do this better (annotation types?)
+ List<String> hideThese = new ArrayList<>();
+ hideThese.add("Temperature Factor");
+ hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ af.getCurrentView().getAlignment(), hideThese, null, false,
+ false);
+ }
+ }
+
protected void processGroovyScript(String id)
{
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);
+ }
}
}
}
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;
}
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;
}
git://source.jalview.org / jalview.git / blobdiff