--paematrix=[label=pAE R4-M5]./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5_scores.json
--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1.pdb
--paematrix=[label=pAE R5-M1]./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json
---image=output1.html
+--image=[textrenderer=text]output1.html
--paematrix=[label=pAE R4-M5]./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5_scores.json
--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1.pdb
--paematrix=[label=pAE R5-M1]./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json
---image=output1.html
+--image=[textrenderer=text]output1.html
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())
+ AlignFrame af = afMap.get(id);
+ while (af != null && af.getViewport().isCalcInProgress())
{
- try {
+ try
+ {
Thread.sleep(25);
- } catch (Exception q) {};
+ } catch (Exception q)
+ {
+ }
+ ;
}
-
+
theseArgsWereParsed &= processImages(id);
if (processLinkedOkay)
theseArgsWereParsed &= processOutput(id);
if ("" != colour)
{
ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
- af.getViewport(), af.getViewport().getAlignment(), colour);
-
- if (cs==null && !"None".equals(colour))
+ af.getViewport(), af.getViewport().getAlignment(),
+ colour);
+
+ if (cs == null && !"None".equals(colour))
+ {
+ Console.warn(
+ "Couldn't parse '" + colour + "' as a colourscheme.");
+ }
+ else
{
- Console.warn("Couldn't parse '"+colour+"' as a colourscheme.");
- } else {
af.changeColour(cs);
}
Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
structureFilepath, tft, paeFilepath, false,
ssFromStructure, false, viewerType);
- if (sv==null)
+ if (sv == null)
{
Console.error("Failed to import and open structure view.");
continue;
}
try
{
- long tries=1000;
- while (sv.isBusy() && tries>0)
+ long tries = 1000;
+ while (sv.isBusy() && tries > 0)
{
Thread.sleep(25);
if (sv.isBusy())
"Waiting for viewer for " + structureFilepath);
}
}
- if (tries==0 && sv.isBusy())
+ if (tries == 0 && sv.isBusy())
{
- Console.warn("Gave up waiting for structure viewer to load. Something may have gone wrong.");
+ Console.warn(
+ "Gave up waiting for structure viewer to load. Something may have gone wrong.");
}
} catch (Exception x)
{
- Console.warn("Exception whilst waiting for structure viewer "+structureFilepath,x);
+ Console.warn("Exception whilst waiting for structure viewer "
+ + structureFilepath, x);
}
- Console.debug("Successfully opened viewer for "+structureFilepath);
+ Console.debug(
+ "Successfully opened viewer for " + structureFilepath);
String structureImageFilename = ArgParser.getValueFromSubValOrArg(
avm, av, Arg.STRUCTUREIMAGE, subVals);
if (sv != null && structureImageFilename != null)
if (sview instanceof AppJmol)
{
AppJmol jmol = (AppJmol) sview;
- try {
- Console.debug("Rendering image to "+structureImageFile);
+ try
+ {
+ Console.debug("Rendering image to " + structureImageFile);
jmol.makePDBImage(structureImageFile, imageType, renderer,
- userBis);
- Console.debug("Finished Rendering image to "+structureImageFile);
+ userBis);
+ Console.debug("Finished Rendering image to "
+ + structureImageFile);
- }
- catch (ImageOutputException ioexc)
+ } catch (ImageOutputException ioexc)
{
- Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc);
+ Console.warn("Unexpected error whilst exporting image to "
+ + structureImageFile, ioexc);
}
}
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
Console.info("Writing " + file);
- try {
- switch (type)
+ try
{
-
- case "svg":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createSVG(file, renderer);
- break;
-
- case "png":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createPNG(file, null, userBis);
- break;
-
- case "html":
- Console.debug("Outputting type '" + type + "' to " + fileName);
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(fileName, renderer);
- break;
-
- case "biojs":
- Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
- try
- {
- BioJsHTMLOutput.refreshVersionInfo(
- BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
- } catch (URISyntaxException e)
+ switch (type)
{
- e.printStackTrace();
+
+ case "svg":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createSVG(file, renderer);
+ break;
+
+ case "png":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createPNG(file, null, userBis);
+ break;
+
+ case "html":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fileName, renderer);
+ break;
+
+ case "biojs":
+ Console.debug(
+ "Creating BioJS MSA Viwer HTML file: " + fileName);
+ try
+ {
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(fileName);
+ break;
+
+ case "eps":
+ Console.debug("Creating EPS file: " + fileName);
+ af.createEPS(file, name);
+ break;
+
+ case "imagemap":
+ Console.debug("Creating ImageMap file: " + fileName);
+ af.createImageMap(file, name);
+ break;
+
+ default:
+ Console.warn(Arg.IMAGE.argString() + " type '" + type
+ + "' not known. Ignoring");
+ break;
}
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(fileName);
- break;
-
- case "eps":
- Console.debug("Creating EPS file: " + fileName);
- af.createEPS(file, name);
- break;
-
- case "imagemap":
- Console.debug("Creating ImageMap file: " + fileName);
- af.createImageMap(file, name);
- break;
-
- default:
- Console.warn(Arg.IMAGE.argString() + " type '" + type
- + "' not known. Ignoring");
- break;
- }
- } catch (Exception ioex) {
- Console.warn("Unexpected error during export",ioex);
+ } catch (Exception ioex)
+ {
+ Console.warn("Unexpected error during export", ioex);
}
}
}
// Also check annotation label widths
if (includeAnnotations && al.getAlignmentAnnotation() != null)
{
- fm = c.getFontMetrics(getAlabels().getFont());
-
- for (i = 0; i < al.getAlignmentAnnotation().length; i++)
+ if (Jalview.isHeadlessMode())
+ {
+ AnnotationLabels aal = this.getAlabels();
+ int stringWidth = aal.drawLabels(null, false, idWidth, false, fm);
+ idWidth = Math.max(idWidth, stringWidth);
+ }
+ else
{
- AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
- if (visibleOnly && !aa.visible)
+ fm = c.getFontMetrics(getAlabels().getFont());
+
+ for (i = 0; i < al.getAlignmentAnnotation().length; i++)
{
- continue;
+ AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+ if (visibleOnly && !aa.visible)
+ {
+ continue;
+ }
+ String label = aa.label;
+ int stringWidth = fm.stringWidth(label);
+ idWidth = Math.max(idWidth, stringWidth);
}
- String label = aa.label;
- int stringWidth = fm.stringWidth(label);
- idWidth = Math.max(idWidth, stringWidth);
}
}
// not be called directly by programs.
// I note that addNotify() is called in several areas of Jalview.
- int annotationHeight = getAnnotationPanel().adjustPanelHeight();
- annotationHeight = getAnnotationPanel()
- .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
+ AnnotationPanel ap = getAnnotationPanel();
+ int annotationHeight = ap.adjustPanelHeight();
+ annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight,
+ annotationHeight);
hscroll.addNotify();
annotationScroller.setPreferredSize(
annotationSpaceFillerHolder.getWidth(), annotationHeight));
annotationScroller.validate();
annotationScroller.addNotify();
+ ap.validate();
}
/**
}
int w = getIdPanel().getWidth();
+ w = this.calculateIdWidth(-1, true, true).width;
return (w > 0 ? w : calculateIdWidth().width);
}
final int borderBottomOffset = 5;
AlignmentDimension aDimension = getAlignmentDimension();
+
// todo use a lambda function in place of callback here?
ImageWriterI writer = new ImageWriterI()
{
*/
package jalview.gui;
+import java.awt.Canvas;
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
private boolean resizePanel = false;
+ private int annotationIdWidth = -1;
+
/**
* Creates a new AnnotationLabels object
*
{
Graphics2D g2d = (Graphics2D) g;
Graphics dummy = g2d.create();
- int annotationIdWidth = drawLabels(dummy, clip, width, false);
+ int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
+ null);
Dimension d = ap.calculateDefaultAlignmentIdWidth();
int alignmentIdWidth = d.width;
if (!iwa.manuallyAdjusted())
{
// If no manual adjustment to ID column with has been made then adjust
// width match widest of alignment or annotation id widths
- width = Math.max(alignmentIdWidth, annotationIdWidth);
+ width = Math.max(alignmentIdWidth, newAnnotationIdWidth);
}
- else if (annotationIdWidth > givenWidth
- && annotationIdWidth > alignmentIdWidth)
+ else if (newAnnotationIdWidth != annotationIdWidth
+ && newAnnotationIdWidth > givenWidth
+ && newAnnotationIdWidth > alignmentIdWidth)
{
// otherwise if the annotation id width has become larger than the
// current id width, increase
- width = annotationIdWidth;
+ width = newAnnotationIdWidth;
+ annotationIdWidth = newAnnotationIdWidth;
}
// set the width if it's changed
if (width != ap.av.getIdWidth())
{
iwa.setWidth(width);
- ap.validateAnnotationDimensions(false);
}
}
- drawLabels(g, clip, width, true);
+ drawLabels(g, clip, width, true, null);
}
/**
* Render the full set of annotation Labels for the alignment at the given
- * cursor. If actuallyDraw is false then no actual drawing will occur, but the
- * widest label width will be returned.
+ * cursor. If actuallyDraw is false or g is null then no actual drawing will
+ * occur, but the widest label width will be returned. If g is null then
+ * fmetrics must be supplied.
+ *
+ * Returns the width of the annotation labels.
*
* @param g
* Graphics2D instance (needed for font scaling)
* rendered
* @param width
* Width for scaling labels
+ * @param fmetrics
+ * FontMetrics if Graphics object g is null
*/
public int drawLabels(Graphics g, boolean clip, int width,
- boolean actuallyDraw)
+ boolean actuallyDraw, FontMetrics fmetrics)
{
int actualWidth = 0;
- if (av.getFont().getSize() < 10)
+ if (actuallyDraw && g != null)
{
- g.setFont(font);
- }
- else
- {
- g.setFont(av.getFont());
+ if (av.getFont().getSize() < 10)
+ {
+ g.setFont(font);
+ }
+ else
+ {
+ g.setFont(av.getFont());
+ }
}
- FontMetrics fm = g.getFontMetrics(g.getFont());
+ FontMetrics fm = fmetrics == null ? g.getFontMetrics(g.getFont())
+ : fmetrics;
if (actuallyDraw)
{
g.setColor(Color.white);
SequenceI lastSeqRef = null;
String lastLabel = null;
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- int fontHeight = g.getFont().getSize();
+ int fontHeight = g != null ? g.getFont().getSize()
+ : fm.getFont().getSize();
int y = 0;
int x = 0;
int graphExtras = 0;
int offset = 0;
- Font baseFont = g.getFont();
+ Font baseFont = g != null ? g.getFont() : fm.getFont();
FontMetrics baseMetrics = fm;
int ofontH = fontHeight;
int sOffset = 0;
continue;
}
}
- if (actuallyDraw)
+ if (actuallyDraw && g != null)
{
g.setColor(Color.black);
}
s = ((float) fontHeight) / (float) ofontH;
Font f = baseFont
.deriveFont(AffineTransform.getScaleInstance(s, s));
- g.setFont(f);
- fm = g.getFontMetrics();
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
- / 2;
+ Canvas c = new Canvas();
+ fm = c.getFontMetrics(f);
+ if (actuallyDraw && g != null)
+ {
+ g.setFont(f);
+ // fm = g.getFontMetrics();
+ graphExtras = (aa[i].height
+ - (groupSize * (fontHeight + 8))) / 2;
+ }
}
}
if (visible)
{
labelWidth = fm.stringWidth(aa[gg].label) + 3;
x = width - labelWidth;
- if (actuallyDraw)
+ if (actuallyDraw && g != null)
{
g.drawString(aa[gg].label, x, y - graphExtras);
}
}
}
- g.setFont(baseFont);
+ if (actuallyDraw && g != null)
+ {
+ g.setFont(baseFont);
+ }
fm = baseMetrics;
fontHeight = ofontH;
}
else
{
- if (actuallyDraw)
+ if (actuallyDraw && g != null)
{
if (vertBar)
{
if (!resizePanel && dragEvent != null && aa != null)
{
- if (actuallyDraw)
+ if (actuallyDraw && g != null)
{
g.setColor(Color.lightGray);
g.drawString(
if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
- if (actuallyDraw)
+ if (actuallyDraw && g != null)
{
g.drawString(MessageManager.getString("label.right_click"), 2, 8);
g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
protected JPanel scalePanelHolder = newJPanel();
- protected JPanel idPanelHolder = newJPanel();
+ public JPanel idPanelHolder = newJPanel();
protected JPanel idSpaceFillerPanel1 = newJPanel();
git://source.jalview.org / jalview.git / commitdiff