</tr>
<tr valign="top">
- <td><code>‑‑title <em>"string""</em></code></td>
+ <td><code>‑‑title <em>"string"</em></code></td>
<td>Specifies the title for the open alignment window as <em>string</em>.</td>
<td></td>
<td align="center">✓</td>
<tr valign="top">
<td><code>‑‑colour <em>name</em></code></td>
- <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em> are:
+ <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em> include:
<br/>
<code>clustal</code>,
<br/>
<code>t-coffee-scores</code>,
<br/>
<code>sequence-id</code>.
+ <br/>
+ <br/>
+ Names of user defined schemes will also work, and jalview colour scheme specifications like:
+ <br/>
+ <code>‑‑colour "D,E=red; K,R,H=0022FF; C,c=yellow"</code>
<td></td>
<td align="center">✓</td>
</tr>
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.FileUtils;
theseArgsWereParsed &= processLinked(id);
processGroovyScript(id);
boolean processLinkedOkay = theseArgsWereParsed;
+
+ // wait around until alignFrame isn't busy
+ AlignFrame af=afMap.get(id);
+ while (af!=null && af.getViewport().isCalcInProgress())
+ {
+ try {
+ Thread.sleep(25);
+ } catch (Exception q) {};
+ }
+
theseArgsWereParsed &= processImages(id);
if (processLinkedOkay)
theseArgsWereParsed &= processOutput(id);
// close ap
if (avm.getBoolean(Arg.CLOSE))
{
- AlignFrame af = afMap.get(id);
+ af = afMap.get(id);
if (af != null)
{
af.closeMenuItem_actionPerformed(true);
Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
if ("" != colour)
{
- af.changeColour_actionPerformed(colour);
+ 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.changeColour(cs);
+ }
Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
}
if (sview instanceof AppJmol)
{
AppJmol jmol = (AppJmol) sview;
- jmol.makePDBImage(structureImageFile, imageType, renderer,
+ try {
+ jmol.makePDBImage(structureImageFile, imageType, renderer,
userBis);
+ }
+ catch (ImageOutputException ioexc)
+ {
+ Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc);
+ }
+
}
break;
default:
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
Console.info("Writing " + file);
-
+ try {
switch (type)
{
break;
case "biojs":
+ Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
try
{
BioJsHTMLOutput.refreshVersionInfo(
}
BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
bjs.exportHTML(fileName);
- Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
break;
case "eps":
- af.createEPS(file, name);
Console.debug("Creating EPS file: " + fileName);
+ af.createEPS(file, name);
break;
case "imagemap":
- af.createImageMap(file, name);
Console.debug("Creating ImageMap file: " + fileName);
+ af.createImageMap(file, name);
break;
default:
+ "' not known. Ignoring");
break;
}
+ } catch (Exception ioex) {
+ Console.warn("Unexpected error during export",ioex);
+ }
}
}
return true;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
ex.printStackTrace(System.err);
}
}
- // TODO - load PDB structure(s) to alignment JAL-629
- // (associate with identical sequence in alignment, or a specified
- // sequence)
+
if (groovyscript != null)
{
// Execute the groovy script after we've done all the rendering stuff
String imageName = "unnamed.png";
while (aparser.getSize() > 1)
{
- String outputFormat = aparser.nextValue();
- file = aparser.nextValue();
-
- if (outputFormat.equalsIgnoreCase("png"))
- {
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("svg"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
+ try
{
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
+ String outputFormat = aparser.nextValue();
+ file = aparser.nextValue();
- System.out.println("Creating HTML image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
- {
- if (file == null)
+ if (outputFormat.equalsIgnoreCase("png"))
{
- System.err.println("The output html file must not be null");
- return;
+ System.out.println("Creating PNG image: " + file);
+ af.createPNG(new File(file));
+ imageName = (new File(file)).getName();
+ continue;
}
- try
+ else if (outputFormat.equalsIgnoreCase("svg"))
{
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
+ System.out.println("Creating SVG image: " + file);
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ af.createSVG(imageFile);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("html"))
{
- e.printStackTrace();
+ File imageFile = new File(file);
+ imageName = imageFile.getName();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+
+ System.out.println("Creating HTML image: " + file);
+ htmlSVG.exportHTML(file);
+ continue;
}
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(file);
- System.out
- .println("Creating BioJS MSA Viwer HTML file: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
- System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
- continue;
- }
- FileFormatI outFormat = null;
- try
- {
- outFormat = FileFormats.getInstance().forName(outputFormat);
- } catch (Exception formatP)
- {
- System.out.println("Couldn't parse " + outFormat
- + " as a valid Jalview format string.");
- }
- if (outFormat != null)
- {
- if (!outFormat.isWritable())
+ else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ {
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ System.out.println(
+ "Creating BioJS MSA Viwer HTML file: " + file);
+ bjs.exportHTML(file);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("imgMap"))
{
+ System.out.println("Creating image map: " + file);
+ af.createImageMap(new File(file), imageName);
+ continue;
+ }
+ else if (outputFormat.equalsIgnoreCase("eps"))
+ {
+ File outputFile = new File(file);
System.out.println(
- "This version of Jalview does not support alignment export as "
- + outputFormat);
+ "Creating EPS file: " + outputFile.getAbsolutePath());
+ af.createEPS(outputFile);
+ continue;
+ }
+
+ FileFormatI outFormat = null;
+ try
+ {
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP)
+ {
+ System.out.println("Couldn't parse " + outFormat
+ + " as a valid Jalview format string.");
}
- else
+ if (outFormat != null)
{
- af.saveAlignment(file, outFormat);
- if (af.isSaveAlignmentSuccessful())
+ if (!outFormat.isWritable())
{
- System.out.println("Written alignment in "
- + outFormat.getName() + " format to " + file);
+ System.out.println(
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
}
else
{
- System.out.println("Error writing file " + file + " in "
- + outFormat.getName() + " format!!");
+ af.saveAlignment(file, outFormat);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in "
+ + outFormat.getName() + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + outFormat.getName() + " format!!");
+ }
}
}
+ } catch (ImageOutputException ioexc)
+ {
+ System.out.println(
+ "Unexpected error whilst exporting image to " + file);
+ ioexc.printStackTrace();
}
}
}
}
- /*
- * testoutput for string values
+ /******************************
+ *
+ * TEST OUTPUT METHODS
+ *
+ ******************************/
+ /**
+ * method for reporting string values parsed/processed during tests
+ *
*/
protected static void testoutput(ArgParser ap, Arg a, String s1,
String s2)
testoutput(true, a, s1, s2);
}
+ /**
+ * method for reporting string values parsed/processed during tests
+ */
+
protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
String s2)
{
testoutput(true, a, s1, s2);
}
+ /**
+ * report value set for string values parsed/processed during tests
+ */
private static void testoutput(boolean yes, Arg a, String s1, String s2)
{
if (yes && ((s1 == null && s2 == null)
"Specifies the title for the open alignment window as string.",
Opt.STRING, Opt.LINKED),
COLOUR(Type.OPENING, "color", // being a bit soft on the Americans!
- "Applies the colour scheme to the open alignment window. Valid values are:\n"
+ "Applies the colour scheme to the open alignment window. Valid values include:\n"
+ "clustal,\n" + "blosum62,\n" + "pc-identity,\n"
+ "zappo,\n" + "taylor,\n" + "gecos-flower,\n"
+ "gecos-blossom,\n" + "gecos-sunset,\n"
+ "turn-propensity,\n" + "buried-index,\n"
+ "nucleotide,\n" + "nucleotide-ambiguity,\n"
+ "purine-pyrimidine,\n" + "rna-helices,\n"
- + "t-coffee-scores,\n" + "sequence-id.",
+ + "t-coffee-scores,\n" + "sequence-id.\n"
+ +"\n"
+ + "Names of user defined colourschemes will also work,\n"
+ +"and jalview colourscheme specifications like\n"
+ +"--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"",
Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.",
Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS),
protected static final String NEGATESTRING = "no";
- // the default linked id prefix used for no id (not even square braces)
+ /**
+ * the default linked id prefix used for no id (ie when not even square braces
+ * are provided)
+ */
protected static final String DEFAULTLINKEDIDPREFIX = "JALVIEW:";
- // the linkedId string used to match all linkedIds seen so far
+ /**
+ * the linkedId string used to match all linkedIds seen so far
+ */
protected static final String MATCHALLLINKEDIDS = "*";
- // the linkedId string used to match all of the last --open'ed linkedIds
+ /**
+ * the linkedId string used to match all of the last --open'ed linkedIds
+ */
protected static final String MATCHOPENEDLINKEDIDS = "open*";
- // the counter added to the default linked id prefix
+ /**
+ * the counter added to the default linked id prefix
+ */
private int defaultLinkedIdCounter = 0;
- // the substitution string used to use the defaultLinkedIdCounter
+ /**
+ * the substitution string used to use the defaultLinkedIdCounter
+ */
private static final String DEFAULTLINKEDIDCOUNTER = "{}";
- // the counter added to the default linked id prefix. NOW using
- // linkedIdAutoCounter
- // private int openLinkedIdCounter = 0;
-
- // the linked id prefix used for --open files. NOW the same as DEFAULT
+ /**
+ * the linked id prefix used for --open files. NOW the same as DEFAULT
+ */
protected static final String OPENLINKEDIDPREFIX = DEFAULTLINKEDIDPREFIX;
- // the counter used for {n} substitutions
+ /**
+ * the counter used for {n} substitutions
+ */
private int linkedIdAutoCounter = 0;
- // the linked id substitution string used to increment the idCounter (and use
- // the incremented value)
+ /**
+ * the linked id substitution string used to increment the idCounter (and use
+ * the incremented value)
+ */
private static final String INCREMENTLINKEDIDAUTOCOUNTER = "{++n}";
- // the linked id substitution string used to use the idCounter
+ /**
+ * the linked id substitution string used to use the idCounter
+ */
private static final String LINKEDIDAUTOCOUNTER = "{n}";
- // the linked id substitution string used to use the filename extension of
- // --append
- // or --open
+ /**
+ * the linked id substitution string used to use the filename extension of
+ * --append or --open
+ */
private static final String LINKEDIDEXTENSION = "{extension}";
- // the linked id substitution string used to use the base filename of --append
- // or --open
+ /**
+ * the linked id substitution string used to use the base filename of --append
+ */
+ /** or --open */
private static final String LINKEDIDBASENAME = "{basename}";
- // the linked id substitution string used to use the dir path of --append
- // or --open
+ /**
+ * the linked id substitution string used to use the dir path of --append or
+ * --open
+ */
private static final String LINKEDIDDIRNAME = "{dirname}";
- // the current argfile
+ /**
+ * the current argfile
+ */
private String argFile = null;
- // the linked id substitution string used to use the dir path of the latest
- // --argfile name
+ /**
+ * the linked id substitution string used to use the dir path of the latest
+ */
+ /** --argfile name */
private static final String ARGFILEBASENAME = "{argfilebasename}";
- // the linked id substitution string used to use the dir path of the latest
- // --argfile name
+ /**
+ * the linked id substitution string used to use the dir path of the latest
+ * --argfile name
+ */
private static final String ARGFILEDIRNAME = "{argfiledirname}";
- // flag to say whether {n} subtitutions in output filenames should be made.
- // Turn on and off with --substitutions and --nosubstitutions
- // Start with it on
+ /**
+ * flag to say whether {n} subtitutions in output filenames should be made.
+ * Turn on and off with --substitutions and --nosubstitutions Start with it on
+ */
private boolean substitutions = true;
- // flag to say whether the default linkedId is the current default linked id
- // or ALL linkedIds
+ /**
+ * flag to say whether the default linkedId is the current default linked id
+ *
+ * or ALL linkedIds
+ */
private boolean allLinkedIds = false;
- // flag to say whether the default linkedId is the current default linked id
- // or OPENED linkedIds
+ /**
+ * flag to say whether the default linkedId is the current default linked id
+ * or OPENED linkedIds
+ */
private boolean openedLinkedIds = false;
- // flag to say whether the structure arguments should be applied to all
- // structures with this linked id
+ /**
+ * flag to say whether the structure arguments should be applied to all
+ * structures with this linked id
+ */
private boolean allStructures = false;
protected static final Map<String, Arg> argMap;
FIRST, BEFORE, AFTER
}
- // get from following Arg of type a or subval of same name (lowercase)
+ /**
+ * get from following Arg of type a or subval of same name (lowercase)
+ */
public static String getValueFromSubValOrArg(ArgValuesMap avm,
ArgValue av, Arg a, SubVals sv)
{
return getFromSubValArgOrPref(avm, av, a, sv, null, null, null);
}
- // get from following Arg of type a or subval key or preference pref or
- // default def
+ /**
+ * get from following Arg of type a or subval key or preference pref or
+ * default def
+ */
public static String getFromSubValArgOrPref(ArgValuesMap avm, ArgValue av,
Arg a, SubVals sv, String key, String pref, String def)
{
def);
}
- // get from following(AFTER), first occurence of (FIRST) or previous (BEFORE)
- // Arg of type a or subval key or preference pref or default def
+ /**
+ * get from following(AFTER), first occurence of (FIRST) or previous (BEFORE)
+ * Arg of type a or subval key or preference pref or default def
+ */
public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
Position pos, ArgValue av, SubVals sv, String key, String pref,
String def)
// the following methods look for the "*" linkedId and add the argvalue to all
// linkedId ArgValues if it does.
- // This version inserts the subvals sv into all created values
+ /**
+ * This version inserts the subvals sv into all created values
+ */
private void addValue(String linkedId, Type type, ArgValues avs,
SubVals sv, String v, int argIndex, boolean doSubs)
{
doSubs);
}
- /*
+ /**
* The following operations look for the "*" and "open*" linkedIds and add the
- * argvalue to all appropriate linkedId ArgValues if it does.
- * If subvals are supplied, they are inserted into all new set values.
+ * argvalue to all appropriate linkedId ArgValues if it does. If subvals are
+ * supplied, they are inserted into all new set values.
*
- * @param op The ArgParser.Op operation
- * @param linkedId The String linkedId from the ArgValuesMap
- * @param type The Arg.Type to attach to this ArgValue
- * @param avs The ArgValues for this linkedId
- * @param sv Use these SubVals on the ArgValue
- * @param merge Merge the SubVals with any existing on the value. False will replace unless sv is null
- * @param v The value of the ArgValue (may contain subvals).
- * @param b The boolean value of the ArgValue.
- * @param argIndex The argIndex for the ArgValue.
- * @param doSubs Whether to perform substitutions on the subvals and value.
+ * @param op
+ * The ArgParser.Op operation
+ * @param linkedId
+ * The String linkedId from the ArgValuesMap
+ * @param type
+ * The Arg.Type to attach to this ArgValue
+ * @param avs
+ * The ArgValues for this linkedId
+ * @param sv
+ * Use these SubVals on the ArgValue
+ * @param merge
+ * Merge the SubVals with any existing on the value. False will
+ * replace unless sv is null
+ * @param v
+ * The value of the ArgValue (may contain subvals).
+ * @param b
+ * The boolean value of the ArgValue.
+ * @param argIndex
+ * The argIndex for the ArgValue.
+ * @param doSubs
+ * Whether to perform substitutions on the subvals and value.
*/
private void argValueOperation(Op op, String linkedId, Type type,
ArgValues avs, SubVals sv, boolean merge, String v, boolean b,
import jalview.io.NewickFile;
import jalview.io.ScoreMatrixFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.io.exceptions.ImageOutputException;
import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
import jalview.project.Jalview2XML;
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
- htmlSVG.exportHTML(null);
+ try {
+ htmlSVG.exportHTML(null);
+ } catch (ImageOutputException x) {
+ // report problem to console and raise dialog
+ }
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+ try {
bjs.exportHTML(null);
+ } catch (ImageOutputException x) {
+ // report problem to console and raise dialog
+ }
}
public void createImageMap(File file, String image)
{
+ try {
alignPanel.makePNGImageMap(file, image);
+ } catch (ImageOutputException x) {
+ // report problem to console and raise dialog
+ }
}
+ @Override
+ public void createPNG_actionPerformed(ActionEvent e) {
+ try{
+ createPNG(null);
+ } catch (ImageOutputException ioex)
+ {
+ // raise dialog, and report via console
+ }
+ }
+ @Override
+ public void createEPS_actionPerformed(ActionEvent e) {
+ try{
+ createEPS(null);
+ } catch (ImageOutputException ioex)
+ {
+ // raise dialog, and report via console
+ }
+
+ }
+ @Override
+ public void createSVG_actionPerformed(ActionEvent e) {
+ try{
+ createSVG(null);
+ } catch (ImageOutputException ioex)
+ {
+ // raise dialog, and report via console
+ }
+
+ }
/**
* Creates a PNG image of the alignment and writes it to the given file. If
* the file is null, the user is prompted to choose a file.
*
* @param f
*/
- @Override
- public void createPNG(File f)
+ public void createPNG(File f) throws ImageOutputException
{
createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
}
- public void createPNG(File f, String renderer, BitmapImageSizing userBis)
+ public void createPNG(File f, String renderer, BitmapImageSizing userBis) throws ImageOutputException
{
alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis);
}
*
* @param f
*/
- @Override
- public void createEPS(File f)
+ public void createEPS(File f) throws ImageOutputException
{
createEPS(f, null);
}
- public void createEPS(File f, String renderer)
+ public void createEPS(File f, String renderer) throws ImageOutputException
{
alignPanel.makeAlignmentImage(TYPE.EPS, f, renderer);
}
*
* @param f
*/
- @Override
- public void createSVG(File f)
+ public void createSVG(File f) throws ImageOutputException
{
createSVG(f, null);
}
- public void createSVG(File f, String renderer)
+ public void createSVG(File f, String renderer) throws ImageOutputException
{
alignPanel.makeAlignmentImage(TYPE.SVG, f, renderer);
}
import jalview.datamodel.SequenceI;
import jalview.gui.ImageExporter.ImageWriterI;
import jalview.io.HTMLOutput;
+import jalview.io.exceptions.ImageOutputException;
import jalview.jbgui.GAlignmentPanel;
import jalview.math.AlignmentDimension;
import jalview.schemes.ResidueProperties;
return (w > 0 ? w : calculateIdWidth().width);
}
- void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
+ void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) throws ImageOutputException
{
makeAlignmentImage(type, file, renderer,
BitmapImageSizing.nullBitmapImageSizing());
* @param bitmapscale
*/
void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer,
- BitmapImageSizing userBis)
+ BitmapImageSizing userBis) throws ImageOutputException
{
final int borderBottomOffset = 5;
}
- public void makePNGImageMap(File imgMapFile, String imageName)
+ public void makePNGImageMap(File imgMapFile, String imageName) throws ImageOutputException
{
// /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
} catch (Exception ex)
{
- ex.printStackTrace();
+ throw new ImageOutputException("couldn't write ImageMap due to unexpected error",ex);
}
} // /////////END OF IMAGE MAP
import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.gui.ImageExporter.ImageWriterI;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.exceptions.ImageOutputException;
import jalview.structure.StructureCommand;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.BrowserLauncher;
@Override
public void makePDBImage(ImageMaker.TYPE type)
{
+ try {
makePDBImage(null, type, null,
BitmapImageSizing.nullBitmapImageSizing());
+ } catch (ImageOutputException ioex) {
+ Console.error("Unexpected error whilst writing "+type.toString(),ioex);
+ }
}
public void makePDBImage(File file, ImageMaker.TYPE type, String renderer,
- BitmapImageSizing userBis)
+ BitmapImageSizing userBis) throws ImageOutputException
{
int width = getWidth();
int height = getHeight();
.toLowerCase(Locale.ROOT);
ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
+
exporter.doExport(file, this, width, height, view, renderer, userBis);
+
}
@Override
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.io.exceptions.ImageOutputException;
import jalview.jbgui.GSplitFrame;
import jalview.jbgui.GStructureViewer;
import jalview.project.Jalview2XML;
String title = "View of desktop";
ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
title);
- exporter.doExport(of, this, width, height, title);
+ try {
+ exporter.doExport(of, this, width, height, title);
+ } catch (ImageOutputException ioex) {
+ jalview.bin.Console.error("Unexpected error whilst writing Jalview desktop snapshot as EPS",ioex);
+ }
}
/**
jalview.bin.Console.debug(Cache.getStackTraceString(e));
}
}
+
+ /**
+ * closes the current instance window, disposes and forgets about it.
+ */
+ public static void closeDesktop()
+ {
+ if (Desktop.instance != null) {
+ Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.instance.setVisible(false);
+ Desktop.instance.dispose();
+ Desktop.instance = null;
+ }
+ }
}
import jalview.bin.Jalview;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.io.exceptions.ImageOutputException;
import jalview.util.ImageMaker;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
* what the image is of e.g. Tree, Alignment
*/
public void doExport(File file, Component parent, int width, int height,
- String imageSource)
+ String imageSource) throws ImageOutputException
{
doExport(file, parent, width, height, imageSource, null,
BitmapImageSizing.nullBitmapImageSizing());
}
public void doExport(File file, Component parent, int width, int height,
- String imageSource, String renderer, BitmapImageSizing userBis)
+ String imageSource, String renderer, BitmapImageSizing userBis) throws ImageOutputException
{
final long messageId = System.currentTimeMillis();
setStatus(
messageId);
} catch (Exception e)
{
- System.out.println(String.format("Error creating %s file: %s", type,
- e.toString()));
+ jalview.bin.Console.error(String.format("Error creating %s file: %s", type,
+ e.toString()),e);
setStatus(MessageManager.formatMessage("info.error_creating_file",
type), messageId);
}
import jalview.datamodel.SequenceI;
import jalview.gui.ImageExporter.ImageWriterI;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.exceptions.ImageOutputException;
import jalview.jbgui.GPCAPanel;
import jalview.math.RotatableMatrix.Axis;
import jalview.util.ImageMaker;
};
String pca = MessageManager.getString("label.pca");
ImageExporter exporter = new ImageExporter(writer, null, type, pca);
- exporter.doExport(null, this, width, height, pca);
+ try {
+ exporter.doExport(null, this, width, height, pca);
+ } catch (ImageOutputException ioex) {
+ Console.error("Unexpected error whilst writing "+type.toString(),ioex);
+ }
}
@Override
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
import jalview.jbgui.GTreePanel;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
String tree = MessageManager.getString("label.tree");
ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
tree);
+ try {
exporter.doExport(null, this, width, height,
tree.toLowerCase(Locale.ROOT));
+ } catch (ImageOutputException ioex) {
+ Console.error("Unexpected error whilst writing "+imageFormat.toString(),ioex);
+ }
}
/**
import jalview.datamodel.AlignmentExportData;
import jalview.gui.AlignmentPanel;
import jalview.gui.IProgressIndicator;
+import jalview.io.exceptions.ImageOutputException;
import jalview.util.MessageManager;
public abstract class HTMLOutput implements Runnable
return generatedFile;
}
- public void exportHTML(String outputFile)
+ public void exportHTML(String outputFile) throws ImageOutputException
{
exportHTML(outputFile, null);
}
- public void exportHTML(String outputFile, String renderer)
+ public void exportHTML(String outputFile, String renderer) throws ImageOutputException
{
setProgressMessage(MessageManager.formatMessage(
"status.exporting_alignment_as_x_file", getDescription()));
}
// used to pass an option such as render to run
- public abstract void run(String string);
+ public abstract void run(String string) throws ImageOutputException;
}
\ No newline at end of file
--- /dev/null
+package jalview.io.exceptions;
+
+/**
+ * wrapper for passing error messages and exceptions back to UI when image io goes wrong
+ * @author jprocter
+ *
+ */
+public class ImageOutputException extends Exception
+{
+
+ public ImageOutputException()
+ {
+ }
+
+ public ImageOutputException(String message)
+ {
+ super(message);
+ }
+
+ public ImageOutputException(Throwable cause)
+ {
+ super(cause);
+ }
+
+ public ImageOutputException(String message, Throwable cause)
+ {
+ super(message, cause);
+ }
+
+ public ImageOutputException(String message, Throwable cause,
+ boolean enableSuppression, boolean writableStackTrace)
+ {
+ super(message, cause, enableSuppression, writableStackTrace);
+ }
+
+}
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.io.FileFormats;
+import jalview.io.exceptions.ImageOutputException;
import jalview.schemes.ResidueColourScheme;
import jalview.util.MessageManager;
import jalview.util.Platform;
@Override
public void actionPerformed(ActionEvent e)
{
- createPNG(null);
+ createPNG_actionPerformed(e);
}
});
createPNG.setActionCommand(
@Override
public void actionPerformed(ActionEvent e)
{
- createEPS(null);
+ createEPS_actionPerformed(e);
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- createSVG(null);
+ createSVG_actionPerformed(e);
}
});
// selectMenu.add(listenToViewSelections);
}
+ protected void createPNG_actionPerformed(ActionEvent object)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void createEPS_actionPerformed(ActionEvent object)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void createSVG_actionPerformed(ActionEvent object)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
protected void copyHighlightedColumns_actionPerformed(
ActionEvent actionEvent)
{
{
}
- public void createPNG(java.io.File f)
- {
- }
protected void font_actionPerformed(ActionEvent e)
{
}
- public void createEPS(java.io.File f)
- {
- }
-
- public void createSVG(java.io.File f)
- {
-
- }
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
@Override
public boolean isWorking()
{
+ boolean working=false;
synchronized (inProgress)
{
// System.err.println("isWorking "+hashCode());
- return inProgress.size() > 0;
+ working |= inProgress.size() > 0;
}
+ synchronized (updating)
+ {
+ for (List<AlignCalcWorkerI> workers : updating.values())
+ {
+ working |= workers.size() > 0;
+ }
+ }
+ return working;
}
@Override
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- if (Desktop.instance != null)
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.closeDesktop();
+ }
+
+ public static void callJalviewMain(String[] args) {
+ if (Jalview.getInstance()!=null) {
+ Jalview.getInstance().doMain(args);
+ } else {
+ Jalview.main(args);
+ }
}
/* --setprops is currently disabled so this test won't work
int numFrames, String[] sequences)
{
String[] args = (cmdLine + " --gui").split("\\s+");
- Jalview.main(args);
+ callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
{
cleanupFiles(filenames);
String[] args = (cmdLine + " --gui").split("\\s+");
- Jalview.main(args);
+ callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
File lastFile = null;
{
cleanupFiles(filenames);
String[] args = (cmdLine + " --gui").split("\\s+");
- Jalview.main(args);
+ callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
File lastFile = null;
String[] nonfilenames)
{
String[] args = (cmdLine + " --gui").split("\\s+");
- Jalview.main(args);
+ callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
for (String filename : filenames)
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- if (Desktop.instance != null)
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.closeDesktop();
}
@Test(
{
String[] args = cmdLine.split("\\s+");
- Jalview.main(args);
+ CommandsTest.callJalviewMain(args);
try
{
// sleep for slow build server to open annotations and viewer windows
git://source.jalview.org / jalview.git / commitdiff