+/*
+ * 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.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
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;
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
-import jalview.bin.argparser.ArgParser.Position;
import jalview.bin.argparser.ArgValue;
import jalview.bin.argparser.ArgValuesMap;
import jalview.bin.argparser.SubVals;
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;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.StringUtils;
import jalview.util.imagemaker.BitmapImageSizing;
public class Commands
private Map<String, AlignFrame> afMap;
+ private Map<String, List<StructureViewer>> svMap;
+
private boolean commandArgsProvided = false;
private boolean argsWereParsed = false;
+ private List<String> errors = new ArrayList<>();
+
public Commands(ArgParser argparser, boolean headless)
{
this(Desktop.instance, argparser, headless);
headless = h;
desktop = d;
afMap = new HashMap<>();
- if (argparser != null)
- {
- processArgs(argparser, headless);
- }
}
- private boolean processArgs(ArgParser argparser, boolean h)
+ protected boolean processArgs()
{
- argParser = argparser;
- headless = h;
+ if (argParser == null)
+ {
+ return true;
+ }
+
boolean theseArgsWereParsed = false;
if (argParser != null && argParser.getLinkedIds() != null)
{
ArgValuesMap avm = argParser.getLinkedArgs(id);
theseArgsWereParsed = true;
- theseArgsWereParsed &= processLinked(id);
+ boolean processLinkedOkay = processLinked(id);
+ theseArgsWereParsed &= processLinkedOkay;
+
processGroovyScript(id);
- boolean processLinkedOkay = theseArgsWereParsed;
// wait around until alignFrame isn't busy
AlignFrame af = afMap.get(id);
}
theseArgsWereParsed &= processImages(id);
+
if (processLinkedOkay)
+ {
theseArgsWereParsed &= processOutput(id);
+ }
// close ap
if (avm.getBoolean(Arg.CLOSE))
}
}
+
+ // 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))
{
- Jalview.getInstance().quit();
+ Jalview.exit("Exiting due to " + Arg.QUIT.argString() + " argument.",
+ ExitCode.OK);
return true;
}
// carry on with jalview.bin.Jalview
return argsWereParsed;
}
- protected boolean processUnlinked(String id)
- {
- return processLinked(id);
- }
-
protected boolean processLinked(String id)
{
boolean theseArgsWereParsed = false;
ArgValuesMap avm = argParser.getLinkedArgs(id);
if (avm == null)
+ {
return true;
+ }
+
+ Boolean isError = Boolean.valueOf(false);
+
+ // 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;
- /*
- * // script to execute after all loading is completed one way or another String
- * groovyscript = m.get(Arg.GROOVY) == null ? null :
- * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
- * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
- * DataSourceType protocol = 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;
}
}
{
if (!(new File(openFile)).exists())
{
- Console.warn("Can't find file '" + openFile + "'");
+ addError("Can't find file '" + openFile + "'");
+ isError = true;
+ continue;
}
}
}
format = new IdentifyFile().identify(openFile, protocol);
} catch (FileFormatException e1)
{
- Console.error("Unknown file format for '" + openFile + "'");
+ addError("Unknown file format for '" + openFile + "'");
+ isError = true;
+ continue;
}
af = afMap.get(id);
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
-
- af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
- format);
-
- // wrap alignment?
- boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
- null, "WRAP_ALIGNMENT", false);
- af.getCurrentView().setWrapAlignment(wrap);
-
- // colour alignment?
- String colour = ArgParser.getFromSubValArgOrPref(avm, av,
- Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
- if ("" != colour)
+ boolean xception = false;
+ try
{
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
- af.getViewport(), af.getViewport().getAlignment(),
- colour);
-
- if (cs == null && !"None".equals(colour))
- {
- Console.warn(
- "Couldn't parse '" + colour + "' as a colourscheme.");
- }
- else
+ af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+ format);
+ } catch (Throwable thr)
+ {
+ xception = true;
+ addError("Couldn't open '" + openFile + "' as " + format + " "
+ + thr.getLocalizedMessage()
+ + " (Enable debug for full stack trace)");
+ isError = true;
+ Console.debug("Exception when opening '" + openFile + "'", thr);
+ } finally
+ {
+ if (af == null && !xception)
{
- af.changeColour(cs);
+ addInfo("Ignoring '" + openFile
+ + "' - no alignment data found.");
+ continue;
}
- Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
}
+ // colour alignment
+ String colour = avm.getFromSubValArgOrPref(av, Arg.COLOUR, sv,
+ null, "DEFAULT_COLOUR_PROT", "");
+ this.colourAlignFrame(af, colour);
+
// Change alignment frame title
- String title = ArgParser.getFromSubValArgOrPref(avm, av,
- Arg.TITLE, sv, null, null, null);
+ String title = avm.getFromSubValArgOrPref(av, Arg.TITLE, sv, null,
+ null, null);
if (title != null)
{
af.setTitle(title);
}
// Add features
- String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av,
+ String featuresfile = avm.getValueFromSubValOrArg(av,
Arg.FEATURES, sv);
if (featuresfile != null)
{
}
// Add annotations from file
- String annotationsfile = ArgParser.getValueFromSubValOrArg(avm,
- av, Arg.ANNOTATIONS, sv);
+ String annotationsfile = avm.getValueFromSubValOrArg(av,
+ Arg.ANNOTATIONS, sv);
if (annotationsfile != null)
{
af.loadJalviewDataFile(annotationsfile, null, null, null);
}
// Set or clear the sortbytree flag
- boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm,
- Arg.SORTBYTREE, sv);
+ boolean sortbytree = avm.getBoolFromSubValOrArg(Arg.SORTBYTREE,
+ sv);
if (sortbytree)
{
af.getViewport().setSortByTree(true);
}
// Load tree from file
- String treefile = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.TREE, sv);
+ String treefile = avm.getValueFromSubValOrArg(av, Arg.TREE, sv);
if (treefile != null)
{
try
"examples/testdata/uniref50_test_tree", treefile);
} catch (IOException e)
{
- Console.warn("Couldn't add tree " + treefile, e);
+ addError("Couldn't add tree " + treefile, e);
+ isError = true;
}
}
// Show secondary structure annotations?
- boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ showSSAnnotations = avm.getFromSubValArgOrPref(
Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
- af.setAnnotationsVisibility(showSSAnnotations, true, false);
-
// Show sequence annotations?
- boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SHOWANNOTATIONS, av.getSubVals(), null,
- "SHOW_ANNOTATIONS", true);
- af.setAnnotationsVisibility(showAnnotations, false, true);
-
- // 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);
- }
+ showAnnotations = avm.getFromSubValArgOrPref(Arg.SHOWANNOTATIONS,
+ av.getSubVals(), null, "SHOW_ANNOTATIONS", true);
+ // hide the Temperature Factor row?
+ hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
+
+ // showSSAnnotations, showAnnotations, hideTFrows used after opening
+ // structure
+
+ // wrap alignment? do this last for formatting reasons
+ wrap = avm.getFromSubValArgOrPref(Arg.WRAP, sv, null,
+ "WRAP_ALIGNMENT", false);
+ // af.setWrapFormat(wrap) is applied after structures are opened for
+ // annotation reasons
// store the AlignFrame for this id
afMap.put(id, af);
{
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);
{
if (headless)
{
- Jalview.exit("Could not open any files in headless mode", 1);
+ Jalview.exit("Could not open any files in headless mode",
+ ExitCode.NO_FILES);
}
else
{
- Console.warn("No more files to open");
+ Console.info("No more files to open");
}
}
if (progressBarSet && desktop != null)
// 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();
- 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
if (seq == null)
{
- Console.warn("Could not find sequence for argument "
+ addWarn("Could not find sequence for argument "
+ Arg.STRUCTURE.argString() + "=" + val);
- // you probably want to continue here, not break
- // break;
continue;
}
+ String structureFilename = null;
File structureFile = null;
if (subVals.getContent() != null
&& subVals.getContent().length() != 0)
{
- structureFile = new File(subVals.getContent());
+ structureFilename = subVals.getContent();
Console.debug("Using structure file (from argument) '"
- + structureFile.getAbsolutePath() + "'");
+ + structureFilename + "'");
+ structureFile = new File(structureFilename);
}
- // TRY THIS
- /*
- * PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE,
- * selectedSequence, true, Desktop.instance);
- *
- * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new
- * SequenceI[] { selectedSequence });
- *
- */
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
&& seq.getAllPDBEntries().size() > 0)
{
structureFile = new File(
seq.getAllPDBEntries().elementAt(0).getFile());
- Console.debug("Using structure file (from sequence) '"
- + structureFile.getAbsolutePath() + "'");
+ if (structureFile != null)
+ {
+ Console.debug("Using structure file (from sequence) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+ structureFilename = structureFile.getAbsolutePath();
}
- if (structureFile == null)
+ if (structureFilename == null || structureFile == null)
{
- Console.warn("Not provided structure file with '" + val + "'");
+ addWarn("Not provided structure file with '" + val + "'");
continue;
}
if (!structureFile.exists())
{
- Console.warn("Structure file '"
- + structureFile.getAbsoluteFile() + "' not found.");
+ addWarn("Structure file '" + structureFile.getAbsoluteFile()
+ + "' not found.");
continue;
}
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
+ argParser.setStructureFilename(structureFilename);
+
// open structure view
AlignmentPanel ap = af.alignPanel;
if (headless)
String structureFilepath = structureFile.getAbsolutePath();
// get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
- String paeFilepath = ArgParser
- .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
- Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
- null, null);
+ String paeFilepath = avm.getFromSubValArgOrPrefWithSubstitutions(
+ argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER,
+ structureAv, subVals, null, null, null);
if (paeFilepath != null)
{
File paeFile = new File(paeFilepath);
} catch (IOException e)
{
paeFilepath = paeFile.getAbsolutePath();
- Console.warn("Problem with the PAE file path: '"
+ addWarn("Problem with the PAE file path: '"
+ paeFile.getPath() + "'");
}
}
// showing annotations from structure file or not
- boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
+ boolean ssFromStructure = avm.getFromSubValArgOrPref(
Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
true);
// get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
// reference annotations
- String tftString = ArgParser
- .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
- Arg.TEMPFAC, Position.AFTER, av, subVals, null,
- null, null);
- boolean notempfac = ArgParser.getFromSubValArgOrPref(avm,
- Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
- true);
+ String tftString = avm.getFromSubValArgOrPrefWithSubstitutions(
+ 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;
if (tftString != null && !notempfac)
{
if (it.hasNext())
sb.append(", ");
}
- Console.warn(sb.toString());
+ addWarn(sb.toString());
}
}
- String sViewer = ArgParser.getFromSubValArgOrPref(avm,
- Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
- null, "jmol");
- ViewerType viewerType = null;
- if (!"none".equals(sViewer))
- {
- for (ViewerType v : EnumSet.allOf(ViewerType.class))
- {
- String name = v.name().toLowerCase(Locale.ROOT)
- .replaceAll(" ", "");
- if (sViewer.equals(name))
- {
- viewerType = v;
- break;
- }
- }
- }
+ String sViewerName = avm.getFromSubValArgOrPref(
+ Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER,
+ structureAv, subVals, null, null, "jmol");
+ ViewerType viewerType = ViewerType.getFromString(sViewerName);
// TODO use ssFromStructure
- StructureViewer sv = StructureChooser
+ StructureViewer structureViewer = StructureChooser
.openStructureFileForSequence(null, null, ap, seq, false,
structureFilepath, tft, paeFilepath, false,
ssFromStructure, false, viewerType);
- if (sv == null)
+ if (structureViewer == null)
{
- Console.error("Failed to import and open structure view.");
+ if (!StringUtils.equalsIgnoreCase(sViewerName, "none"))
+ {
+ addError("Failed to import and open structure view for file '"
+ + structureFile + "'.");
+ }
continue;
}
try
{
long tries = 1000;
- while (sv.isBusy() && tries > 0)
+ while (structureViewer.isBusy() && tries > 0)
{
Thread.sleep(25);
- if (sv.isBusy())
+ if (structureViewer.isBusy())
{
tries--;
Console.debug(
"Waiting for viewer for " + structureFilepath);
}
}
- if (tries == 0 && sv.isBusy())
+ if (tries == 0 && structureViewer.isBusy())
{
- Console.warn(
- "Gave up waiting for structure viewer to load. Something may have gone wrong.");
+ addWarn("Gave up waiting for structure viewer to load file '"
+ + structureFile
+ + "'. Something may have gone wrong.");
}
} catch (Exception x)
{
- Console.warn("Exception whilst waiting for structure viewer "
+ addError("Exception whilst waiting for structure viewer "
+ structureFilepath, x);
+ isError = true;
}
+
+ // add StructureViewer to svMap list
+ if (svMap == null)
+ {
+ svMap = new HashMap<>();
+ }
+ if (svMap.get(id) == null)
+ {
+ svMap.put(id, new ArrayList<>());
+ }
+ svMap.get(id).add(structureViewer);
+
Console.debug(
"Successfully opened viewer for " + structureFilepath);
- String structureImageFilename = ArgParser.getValueFromSubValOrArg(
- avm, av, Arg.STRUCTUREIMAGE, subVals);
- if (sv != null && structureImageFilename != null)
- {
- ArgValue siAv = avm.getClosestNextArgValueOfArg(av,
- Arg.STRUCTUREIMAGE);
- SubVals sisv = null;
- if (structureImageFilename.equals(siAv.getValue()))
- {
- sisv = siAv.getSubVals();
- }
- File structureImageFile = new File(structureImageFilename);
- String width = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.STRUCTUREIMAGEWIDTH, sisv);
- String height = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.STRUCTUREIMAGEHEIGHT, sisv);
- String scale = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.STRUCTUREIMAGESCALE, sisv);
- String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
- String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.STRUCTUREIMAGETYPE, sisv);
- if (typeS == null || typeS.length() == 0)
- {
- typeS = FileUtils.getExtension(structureImageFile);
- }
- TYPE imageType;
- try
- {
- imageType = Enum.valueOf(TYPE.class,
- typeS.toUpperCase(Locale.ROOT));
- } catch (IllegalArgumentException e)
- {
- Console.warn("Do not know image format '" + typeS
- + "', using PNG");
- imageType = TYPE.PNG;
- }
- BitmapImageSizing userBis = ImageMaker
- .parseScaleWidthHeightStrings(scale, width, height);
- // TODO MAKE THIS VIEWER INDEPENDENT!!
- switch (StructureViewer.getViewerType())
+
+ if (avm.containsArg(Arg.STRUCTUREIMAGE))
+ {
+ for (ArgValue structureImageArgValue : avm
+ .getArgValueListFromSubValOrArg(structureAv,
+ Arg.STRUCTUREIMAGE, subVals))
{
- case JMOL:
- try
- {
- Thread.sleep(1000); // WHY ???
- } catch (InterruptedException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- JalviewStructureDisplayI sview = sv
- .getJalviewStructureDisplay();
- if (sview instanceof AppJmol)
+ String structureImageFilename = argParser.makeSubstitutions(
+ structureImageArgValue.getValue(), id, true);
+ if (structureViewer != null && structureImageFilename != null)
{
- AppJmol jmol = (AppJmol) sview;
+ SubVals structureImageSubVals = null;
+ structureImageSubVals = structureImageArgValue.getSubVals();
+ File structureImageFile = new File(structureImageFilename);
+ String width = avm.getValueFromSubValOrArg(
+ structureImageArgValue, Arg.WIDTH,
+ structureImageSubVals);
+ String height = avm.getValueFromSubValOrArg(
+ structureImageArgValue, Arg.HEIGHT,
+ structureImageSubVals);
+ String scale = avm.getValueFromSubValOrArg(
+ structureImageArgValue, Arg.SCALE,
+ structureImageSubVals);
+ String renderer = avm.getValueFromSubValOrArg(
+ structureImageArgValue, Arg.TEXTRENDERER,
+ structureImageSubVals);
+ String typeS = avm.getValueFromSubValOrArg(
+ structureImageArgValue, Arg.TYPE,
+ structureImageSubVals);
+ if (typeS == null || typeS.length() == 0)
+ {
+ typeS = FileUtils.getExtension(structureImageFile);
+ }
+ TYPE imageType;
try
{
- Console.debug("Rendering image to " + structureImageFile);
+ imageType = Enum.valueOf(TYPE.class,
+ typeS.toUpperCase(Locale.ROOT));
+ } catch (IllegalArgumentException e)
+ {
+ addWarn("Do not know image format '" + typeS
+ + "', using PNG");
+ imageType = TYPE.PNG;
+ }
+ 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);
+ ColourSchemeI originalColourScheme = this
+ .getColourScheme(af);
+ this.colourAlignFrame(af, imageColour);
+
+ /////
+ // custom image background colour
+
+ String bgcolourstring = avm.getValueFromSubValOrArg(
+ structureImageArgValue, Arg.BGCOLOUR,
+ structureImageSubVals);
+ Color bgcolour = null;
+ if (bgcolourstring != null && bgcolourstring.length() > 0)
+ {
+ bgcolour = ColorUtils.parseColourString(bgcolourstring);
+ if (bgcolour == null)
+ {
+ Console.warn(
+ "Background colour string '" + bgcolourstring
+ + "' not recognised -- using default");
+ }
+ }
+
+ 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)
+ {
+ 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.debug("Finished Rendering image to "
+ Console.info("Exported structure image to "
+ structureImageFile);
- } catch (ImageOutputException ioexc)
+ // RESTORE SESSION AFTER EXPORT IF NEED BE
+ if (sessionToRestore != null)
+ {
+ Console.debug(
+ "Restoring session from " + sessionToRestore);
+
+ sview.getBinding().restoreSession(
+ sessionToRestore.getAbsolutePath());
+
+ }
+ } catch (ImageOutputException ioexec)
{
- Console.warn("Unexpected error whilst exporting image to "
- + structureImageFile, ioexc);
+ 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);
+ }
}
-
}
- break;
- default:
- Console.warn("Cannot export image for structure viewer "
- + sv.getViewerType() + " yet");
- break;
}
}
+ 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)
+ {
+ 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;
+ 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))
{
- Console.warn("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)
{
- Console.warn("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;
}
+ Boolean isError = Boolean.valueOf(false);
if (avm.containsArg(Arg.IMAGE))
{
- for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
+ for (ArgValue imageAv : avm.getArgValueList(Arg.IMAGE))
{
- String val = av.getValue();
- SubVals subVal = av.getSubVals();
- String fileName = subVal.getContent();
+ String val = imageAv.getValue();
+ SubVals imageSubVals = imageAv.getSubVals();
+ String fileName = imageSubVals.getContent();
File file = new File(fileName);
String name = af.getName();
- String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.TEXTRENDERER, subVal);
+ String renderer = avm.getValueFromSubValOrArg(imageAv,
+ Arg.TEXTRENDERER, imageSubVals);
if (renderer == null)
renderer = "text";
String type = "png"; // default
- String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE,
- subVal);
- String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH,
- subVal);
- String height = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.HEIGHT, subVal);
+ String scale = avm.getValueFromSubValOrArg(imageAv, Arg.SCALE,
+ imageSubVals);
+ String width = avm.getValueFromSubValOrArg(imageAv, Arg.WIDTH,
+ imageSubVals);
+ String height = avm.getValueFromSubValOrArg(imageAv, Arg.HEIGHT,
+ imageSubVals);
BitmapImageSizing userBis = ImageMaker
.parseScaleWidthHeightStrings(scale, width, height);
- type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
+ type = avm.getValueFromSubValOrArg(imageAv, Arg.TYPE, imageSubVals);
if (type == null && fileName != null)
{
for (String ext : new String[] { "svg", "png", "html", "eps" })
Cache.setPropsAreReadOnly(true);
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+ String imageColour = avm.getValueFromSubValOrArg(imageAv,
+ Arg.IMAGECOLOUR, imageSubVals);
+ ColourSchemeI originalColourScheme = this.getColourScheme(af);
+ this.colourAlignFrame(af, imageColour);
+
Console.info("Writing " + file);
+
+ boolean success = checksBeforeWritingToFile(avm, imageSubVals,
+ false, fileName, "image", isError);
+ if (!success)
+ {
+ continue;
+ }
+
try
{
switch (type)
case "biojs":
Console.debug(
- "Creating BioJS MSA Viwer HTML file: " + fileName);
+ "Outputting BioJS MSA Viwer HTML file: " + fileName);
try
{
BioJsHTMLOutput.refreshVersionInfo(
break;
case "eps":
- Console.debug("Creating EPS file: " + fileName);
- af.createEPS(file, name);
+ Console.debug("Outputting EPS file: " + fileName);
+ af.createEPS(file, renderer);
break;
case "imagemap":
- Console.debug("Creating ImageMap file: " + fileName);
+ Console.debug("Outputting ImageMap file: " + fileName);
af.createImageMap(file, name);
break;
default:
- Console.warn(Arg.IMAGE.argString() + " type '" + type
+ addWarn(Arg.IMAGE.argString() + " type '" + type
+ "' not known. Ignoring");
break;
}
} catch (Exception ioex)
{
- Console.warn("Unexpected error during export", ioex);
+ addError("Unexpected error during export to '" + fileName + "'",
+ ioex);
+ isError = true;
}
+
+ this.colourAlignFrame(af, originalColourScheme);
}
}
- return true;
+ return !isError;
}
protected boolean processOutput(String id)
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)
{
- Console.warn("Did not have an alignment window for id=" + id);
+ addWarn("Do not have an alignment window (id=" + id
+ + "). Not proceeding.");
return false;
}
+ Boolean isError = Boolean.valueOf(false);
+
if (avm.containsArg(Arg.OUTPUT))
{
for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
String val = av.getValue();
SubVals subVals = av.getSubVals();
String fileName = subVals.getContent();
- boolean stdout = fileName.equals("-");
+ boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
File file = new File(fileName);
- boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
- Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
- // backups. Use the Arg.BACKUPS or subval "backups" setting first,
- // otherwise if headless assume false, if not headless use the user
- // preference with default true.
- boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
- subVals, null,
- Platform.isHeadless() ? null : BackupFiles.ENABLED,
- !Platform.isHeadless());
-
- // if backups is not true then --overwrite must be specified
- if (file.exists() && !(overwrite || backups || stdout))
- {
- Console.error("Won't overwrite file '" + fileName + "' without "
- + Arg.OVERWRITE.argString() + " or "
- + Arg.BACKUPS.argString() + " set");
- return false;
- }
String name = af.getName();
- String format = ArgParser.getValueFromSubValOrArg(avm, av,
- Arg.FORMAT, subVals);
+ String format = avm.getValueFromSubValOrArg(av, Arg.FORMAT,
+ subVals);
FileFormats ffs = FileFormats.getInstance();
List<String> validFormats = ffs.getWritableFormats(false);
validSB.append(")");
}
- Jalview.exit("No valid format specified for "
+ addError("No valid format specified for "
+ Arg.OUTPUT.argString() + ". Valid formats are "
- + validSB.toString() + ".", 1);
- // this return really shouldn't happen
- return false;
+ + validSB.toString() + ".");
+ continue;
}
}
- String savedBackupsPreference = Cache
- .getDefault(BackupFiles.ENABLED, null);
- Console.debug("Setting backups to " + backups);
- Cache.applicationProperties.put(BackupFiles.ENABLED,
- Boolean.toString(backups));
+ boolean success = checksBeforeWritingToFile(avm, subVals, true,
+ fileName, ff.getName(), isError);
+ if (!success)
+ {
+ continue;
+ }
+
+ boolean backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVals,
+ null, Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
Console.info("Writing " + fileName);
- af.saveAlignment(fileName, ff, stdout);
- Console.debug("Returning backups to " + savedBackupsPreference);
- if (savedBackupsPreference != null)
- Cache.applicationProperties.put(BackupFiles.ENABLED,
- savedBackupsPreference);
+ af.saveAlignment(fileName, ff, stdout, backups);
if (af.isSaveAlignmentSuccessful())
{
Console.debug("Written alignment '" + name + "' in "
- + ff.getName() + " format to " + file);
+ + ff.getName() + " format to '" + file + "'");
}
else
{
- Console.warn("Error writing file " + file + " in " + ff.getName()
+ addError("Error writing file '" + file + "' in " + ff.getName()
+ " format!");
+ isError = true;
+ continue;
}
}
}
- return true;
+ return !isError;
}
private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
ArgValue av)
{
SubVals subVals = av.getSubVals();
- ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
+ ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID, true);
SequenceI seq = null;
if (subVals == null && idAv == null)
return null;
seq = al.getSequenceAt(subVals.getIndex());
}
}
- else if (idAv != null)
+ if (seq == null && idAv != null)
{
seq = al.findName(idAv.getValue());
}
return seq;
}
+
+ public AlignFrame[] getAlignFrames()
+ {
+ AlignFrame[] afs = null;
+ if (afMap != null)
+ {
+ afs = (AlignFrame[]) afMap.values().toArray();
+ }
+
+ return afs;
+ }
+
+ public List<StructureViewer> getStructureViewers()
+ {
+ List<StructureViewer> svs = null;
+ if (svMap != null)
+ {
+ for (List<StructureViewer> svList : svMap.values())
+ {
+ if (svs == null)
+ {
+ svs = new ArrayList<>();
+ }
+ svs.addAll(svList);
+ }
+ }
+ return svs;
+ }
+
+ private void colourAlignFrame(AlignFrame af, String colour)
+ {
+ // use string "none" to remove colour scheme
+ if (colour != null && "" != colour)
+ {
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), colour);
+ if (cs == null && !StringUtils.equalsIgnoreCase(colour, "none"))
+ {
+ addWarn("Couldn't parse '" + colour + "' as a colourscheme.");
+ }
+ else
+ {
+ Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
+ colourAlignFrame(af, cs);
+ }
+ }
+ }
+
+ private void colourAlignFrame(AlignFrame af, ColourSchemeI cs)
+ {
+ // Note that cs == null removes colour scheme from af
+ af.changeColour(cs);
+ }
+
+ private ColourSchemeI getColourScheme(AlignFrame af)
+ {
+ return af.getViewport().getGlobalColourScheme();
+ }
+
+ private void addInfo(String errorMessage)
+ {
+ Console.info(errorMessage);
+ errors.add(errorMessage);
+ }
+
+ private void addWarn(String errorMessage)
+ {
+ Console.warn(errorMessage);
+ errors.add(errorMessage);
+ }
+
+ private void addError(String errorMessage)
+ {
+ addError(errorMessage, null);
+ }
+
+ private void addError(String errorMessage, Exception e)
+ {
+ Console.error(errorMessage, e);
+ errors.add(errorMessage);
+ }
+
+ private boolean checksBeforeWritingToFile(ArgValuesMap avm,
+ SubVals subVal, boolean includeBackups, String filename,
+ String adjective, Boolean isError)
+ {
+ File file = new File(filename);
+
+ boolean overwrite = avm.getFromSubValArgOrPref(Arg.OVERWRITE, subVal,
+ null, "OVERWRITE_OUTPUT", false);
+ boolean stdout = false;
+ boolean backups = false;
+ if (includeBackups)
+ {
+ stdout = ArgParser.STDOUTFILENAME.equals(filename);
+ // backups. Use the Arg.BACKUPS or subval "backups" setting first,
+ // otherwise if headless assume false, if not headless use the user
+ // preference with default true.
+ backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVal, null,
+ Platform.isHeadless() ? null : BackupFiles.ENABLED,
+ !Platform.isHeadless());
+ }
+
+ if (file.exists() && !(overwrite || backups || stdout))
+ {
+ addWarn("Won't overwrite file '" + filename + "' without "
+ + Arg.OVERWRITE.argString()
+ + (includeBackups ? " or " + Arg.BACKUPS.argString() : "")
+ + " set");
+ return false;
+ }
+
+ boolean mkdirs = avm.getFromSubValArgOrPref(Arg.MKDIRS, subVal, null,
+ "MKDIRS_OUTPUT", false);
+
+ if (!FileUtils.checkParentDir(file, mkdirs))
+ {
+ addError("Directory '"
+ + FileUtils.getParentDir(file).getAbsolutePath()
+ + "' does not exist for " + adjective + " file '" + filename
+ + "'."
+ + (mkdirs ? "" : " Try using " + Arg.MKDIRS.argString()));
+ isError = true;
+ return false;
+ }
+
+ return true;
+ }
+
+ public List<String> getErrors()
+ {
+ return errors;
+ }
+
+ public String errorsToString()
+ {
+ StringBuilder sb = new StringBuilder();
+ for (String error : errors)
+ {
+ if (sb.length() > 0)
+ sb.append("\n");
+ sb.append("- " + error);
+ }
+ return sb.toString();
+ }
}
git://source.jalview.org / jalview.git / blobdiff