{
// props file provided as URL
fis = new URL(propertiesFile).openStream();
- System.out.println(
- "Loading jalview properties from : " + propertiesFile);
- System.out.println(
- "Disabling Jalview writing to user's local properties file.");
+ if (!Jalview.quiet())
+ {
+ System.out.println(
+ "Loading jalview properties from : " + propertiesFile);
+ System.out.println(
+ "Disabling Jalview writing to user's local properties file.");
+ }
propsAreReadOnly = true;
} catch (Exception ex)
{
fis.close();
} catch (Exception ex)
{
- System.out.println("Error reading properties file: " + ex);
+ if (!Jalview.quiet())
+ System.out.println("Error reading properties file: " + ex);
}
}
}
} catch (Exception ex)
{
- System.out.println("Error reading author details: " + ex);
+ if (!Jalview.quiet())
+ System.out.println("Error reading author details: " + ex);
authorDetails = null;
}
if (authorDetails == null)
remoteVersion = remoteBuildProperties.getProperty("VERSION");
} catch (Exception ex)
{
- System.out.println(
- "Non-fatal exception when checking version at "
- + remoteBuildPropertiesUrl + ":");
- System.out.println(ex);
+ if (!Jalview.quiet())
+ {
+ System.out.println(
+ "Non-fatal exception when checking version at "
+ + remoteBuildPropertiesUrl + ":");
+ System.out.println(ex);
+ }
remoteVersion = getProperty("VERSION");
}
}
}
} catch (Exception ex)
{
- System.out.println("Error reading build details: " + ex);
+ if (!Jalview.quiet())
+ System.out.println("Error reading build details: " + ex);
applicationProperties.remove("VERSION");
}
String codeVersion = getProperty("VERSION");
new BuildDetails(codeVersion, null, codeInstallation);
if (printVersion && reportVersion)
{
- if (!Jalview.quiet())
- {
- System.out.println(ChannelProperties.getProperty("app_name")
- + " Version: " + codeVersion + codeInstallation);
- }
+ System.out.println(ChannelProperties.getProperty("app_name")
+ + " version: " + codeVersion + codeInstallation);
}
}
def = Integer.parseInt(string);
} catch (NumberFormatException e)
{
- System.out.println("Error parsing int property '" + property
- + "' with value '" + string + "'");
+ if (!Jalview.quiet())
+ System.out.println("Error parsing int property '" + property
+ + "' with value '" + string + "'");
}
}
}
} catch (Exception ex)
{
- System.out.println(
- "Error setting property: " + key + " " + obj + "\n" + ex);
+ if (!Jalview.quiet())
+ System.out.println(
+ "Error setting property: " + key + " " + obj + "\n" + ex);
}
return oldValue;
}
out.close();
} catch (Exception ex)
{
- System.out.println("Error saving properties: " + ex);
+ if (!Jalview.quiet())
+ System.out.println("Error saving properties: " + ex);
}
}
}
}
} catch (Exception ex)
{
- System.out.println("Error loading User ColourFile\n" + ex);
+ if (!Jalview.quiet())
+ System.out.println("Error loading User ColourFile\n" + ex);
}
}
if (!files.equals(coloursFound.toString()))
// 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.getBoolFromSubValOrArg(avm,
+ Arg.NOTEMPFAC, subVals);
+ TFType tft = notempfac ? null : TFType.DEFAULT;
+ /*
String tftString = subVals.get("tempfac");
- TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
- : TFType.DEFAULT;
ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
af, structureFilepath);
if (tftString == null && tftAv != null)
{
tftString = tftAv.getSubVals().getContent();
}
- if (tftString != null)
+ */
+ if (tftString != null && !notempfac)
{
// get kind of temperature factor annotation
try
}
}
- boolean addTempFac = tft != null
- || Cache.getDefault("ADD_TEMPFACT_ANN", false);
+ boolean addTempFac = notempfac ? false
+ : ((tft != null)
+ || Cache.getDefault("ADD_TEMPFACT_ANN", false));
// TODO use ssFromStructure
StructureChooser.openStructureFileForSequence(null, null, ap, seq,
if (renderer == null)
renderer = "text";
String type = "png"; // default
+
+ float bitmapscale = 0.0f;
+ int bitmapwidth = 0;
+ int bitmapheight = 0;
+ String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE,
+ subVal);
+ if (scale != null)
+ {
+ try
+ {
+ bitmapscale = Float.parseFloat(scale);
+ } catch (NumberFormatException e)
+ {
+ Console.warn("Did not understand scale '" + scale
+ + "', won't be used.");
+ }
+ }
+ String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH,
+ subVal);
+ if (width != null)
+ {
+ try
+ {
+ bitmapwidth = Integer.parseInt(width);
+ } catch (NumberFormatException e)
+ {
+ Console.warn("Did not understand width '" + width
+ + "', won't be used.");
+ }
+ }
+ String height = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.HEIGHT, subVal);
+ if (height != null)
+ {
+ try
+ {
+ bitmapheight = Integer.parseInt(height);
+ } catch (NumberFormatException e)
+ {
+ Console.warn("Did not understand height '" + height
+ + "', won't be used.");
+ }
+ }
+
type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
if (type == null && fileName != null)
{
case "png":
Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createPNG(file);
+ af.createPNG(file, null, bitmapscale, bitmapwidth, bitmapheight);
break;
case "html":
}
}
- if (bootstrapArgs.contains(Arg.HELP))
+ if (bootstrapArgs.contains(Arg.HELP)
+ || bootstrapArgs.contains(Arg.VERSION))
{
QUIET = true;
}
}.start();
}
- if (!quiet())
+ if (!quiet() || bootstrapArgs.contains(Arg.VERSION))
{
System.out.println(
"Java version: " + System.getProperty("java.version"));
- System.out.println("Java Home: " + System.getProperty("java.home"));
- System.out.println(System.getProperty("os.arch") + " "
+ System.out.println("Java home: " + System.getProperty("java.home"));
+ System.out.println("Java arch: " + System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
.bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
// report Jalview version
- Cache.loadBuildProperties(true);
+ Cache.loadBuildProperties(
+ !quiet() || bootstrapArgs.contains(Arg.VERSION));
+
+ // stop now if only after --version
+ if (bootstrapArgs.contains(Arg.VERSION))
+ {
+ Jalview.exit(null, 0);
+ }
// old ArgsParser
ArgsParser aparser = new ArgsParser(args);
// Initialising arguments (BOOTSTRAP)
HELP("Display this help statement", Opt.UNARY, Opt.BOOTSTRAP),
+ VERSION("Display the version of "
+ + ChannelProperties.getProperty("app_name"), Opt.UNARY,
+ Opt.BOOTSTRAP),
HEADLESS(
"Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.",
Opt.UNARY, Opt.BOOTSTRAP),
Opt.STRING, Opt.LINKED, Opt.MULTI),
NOTEMPFAC(
"Do not show the temperature factor annotation for the preceding --structure.",
- Opt.UNARY, Opt.LINKED),
+ Opt.UNARY, Opt.LINKED, Opt.SECRET), // keep this secret until it
+ // works!
SHOWSSANNOTATIONS(null, Opt.BOOLEAN, Opt.LINKED),
// Outputting files
"Sets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values for name are:\n"
+ "text,\n" + "lineart.",
Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ SCALE("Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. If used in conjunction with --width and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ WIDTH("Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
+ HEIGHT("Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --scale and --width then the smallest scaling will be used (scale, width and height provide bounds for the image).",
+ Opt.STRING, Opt.LINKED, Opt.ALLOWALL),
OUTPUT("Export the open alignment to file filename. The format name is specified by the subval modifier format=name, a following --format name argument or guessed from the file extension. Valid format names (and file extensions) are:\n"
+ "fasta (fa, fasta, mfa, fastq),\n" + "pfam (pfam),\n"
+ "stockholm (sto, stk),\n" + "pir (pir),\n" + "blc (blc),\n"
options.add("allows substitutions");
}
+ if (a.hasOption(Opt.ALLOWALL))
+ {
+ options.add("can be applied to all linked arguments");
+ }
+
if (a.hasOption(Opt.PRIVATE))
{
options.add("for internal use only");
{
// arg not found
Console.error("Argument '" + arg + "' not recognised. Exiting.");
- Jalview.exit("Unrecognised command line argument '" + arg + "'",
- 13);
+ Jalview.exit("Invalid argument used." + System.lineSeparator()
+ + "Use" + System.lineSeparator() + "jalview "
+ + Arg.HELP.argString() + System.lineSeparator()
+ + "for a usage statement.", 13);
continue;
}
if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
package jalview.datamodel.annotations;
import jalview.datamodel.Annotation;
-import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.TFType;
public class AnnotationRowBuilder
/**
* the type of temperature factor plot (if it is one)
*/
- private StructureImportSettings.TFType tfType = StructureImportSettings.TFType.DEFAULT;
+ // private TFType tfType = TFType.DEFAULT;
+ private TFType tfType = null;
- public void setTFType(StructureImportSettings.TFType t)
+ public void setTFType(TFType t)
{
tfType = t;
}
- public StructureImportSettings.TFType getTFType()
+ public TFType getTFType()
{
return tfType;
}
name = string;
}
- public AnnotationRowBuilder(String name, float min, float max, StructureImportSettings.TFType tft)
+ public AnnotationRowBuilder(String name, float min, float max, TFType tft)
{
this(name, min, max);
setTFType(tft);
@Override
public void createPNG(File f)
{
- createPNG(f, null);
+ createPNG(f, null, 0.0f, 0, 0);
}
- public void createPNG(File f, String renderer)
+ public void createPNG(File f, String renderer, float bitmapscale,
+ int bitmapwidth, int bitmapheight)
{
- alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer);
+ alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, bitmapscale,
+ bitmapwidth, bitmapheight);
}
/**
return (w > 0 ? w : calculateIdWidth().width);
}
+ void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
+ {
+ makeAlignmentImage(type, file, renderer, 0.0f, 0, 0);
+ }
+
/**
* Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
* writes it to the specified file
*
* @param type
* @param file
+ * @param textrenderer
+ * @param bitmapscale
*/
- void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
+ void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer,
+ float bitmapscale, int bitmapwidth, int bitmapheight)
{
final int borderBottomOffset = 5;
int imageWidth = aDimension.getWidth();
int imageHeight = aDimension.getHeight() + borderBottomOffset;
String of = MessageManager.getString("label.alignment");
- exporter.doExport(file, this, imageWidth, imageHeight, of, renderer);
+ exporter.doExport(file, this, imageWidth, imageHeight, of, renderer,
+ bitmapscale, bitmapwidth, bitmapheight);
}
/**
public void doExport(File file, Component parent, int width, int height,
String imageSource)
{
- doExport(file, parent, width, height, imageSource, null);
+ doExport(file, parent, width, height, imageSource, null, 0.0f, 0, 0);
}
public void doExport(File file, Component parent, int width, int height,
- String imageSource, String renderer)
+ String imageSource, String renderer, float bitmapscale,
+ int bitmapwidth, int bitmapheight)
{
final long messageId = System.currentTimeMillis();
setStatus(
final File chosenFile = file;
Callable<Void> okAction = () -> {
exportImage(chosenFile, !textSelected.get(), width, height,
- messageId);
+ messageId, bitmapscale, bitmapwidth, bitmapheight);
return null;
};
LineartOptions epsOption = new LineartOptions(TYPE.EPS.getName(),
* character rendering not required, or preference already set
* - just do the export
*/
- exportImage(file, !textSelected.get(), width, height, messageId);
+ exportImage(file, !textSelected.get(), width, height, messageId,
+ bitmapscale, bitmapwidth, bitmapheight);
}
}
* @param messageId
*/
protected void exportImage(File chosenFile, boolean asLineart, int width,
- int height, long messageId)
+ int height, long messageId, float bitmapscale, int bitmapwidth,
+ int bitmapheight)
{
String type = imageType.getName();
try
// "status.exporting_alignment_as_x_file", type),
// messageId);
ImageMaker im = new ImageMaker(imageType, width, height, chosenFile,
- title, asLineart);
+ title, asLineart, bitmapscale, bitmapwidth, bitmapheight);
imageWriter.exportImage(im.getGraphics());
im.writeImage();
setStatus(
private boolean pdbIdAvailable;
- private StructureImportSettings.TFType temperatureFactorType = TFType.DEFAULT;
+ private TFType temperatureFactorType = TFType.DEFAULT;
private String paeMatrix = null;
return paeMatrix != null;
}
- public void setTemperatureFactorType(StructureImportSettings.TFType t)
+ public void setTemperatureFactorType(TFType t)
{
this.temperatureFactorType = t;
}
- public StructureImportSettings.TFType getTemperatureFactorType()
+ public TFType getTemperatureFactorType()
{
return temperatureFactorType;
}
}
public StructureFile(Object inFile, DataSourceType sourceType,
- StructureImportSettings.TFType tempfacType) throws IOException
+ TFType tempfacType) throws IOException
{
super(false, inFile, sourceType);
this.setTemperatureFactorType(tempfacType);
*/
package jalview.util;
-import jalview.io.JalviewFileChooser;
-
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import org.jfree.graphics2d.svg.SVGHints;
import org.jibble.epsgraphics.EpsGraphics2D;
+import jalview.io.JalviewFileChooser;
+
public class ImageMaker
{
public static final String SVG_DESCRIPTION = "Scalable Vector Graphics";
* @param file
* @param fileTitle
* @param useLineart
+ * @param bitmapscale
* @throws IOException
*/
public ImageMaker(TYPE imageType, int width, int height, File file,
- String fileTitle, boolean useLineart) throws IOException
+ String fileTitle, boolean useLineart, float bitmapscale,
+ int bitmapwidth, int bitmapheight) throws IOException
{
this.type = imageType;
setupEPS(width, height, fileTitle, useLineart);
break;
case PNG:
- setupPNG(width, height);
+ setupPNG(width, height, bitmapscale, bitmapwidth, bitmapheight);
break;
default:
}
*
* @param width
* @param height
+ * @param scale
*/
- protected void setupPNG(int width, int height)
+ protected void setupPNG(int width, int height, float scale,
+ int bitmapwidth, int bitmapheight)
{
- bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+ if (width == 0 || height == 0)
+ return;
+
+ float usescale = 0.0f;
+ int usewidth = width;
+ int useheight = height;
+
+ // use the smallest positive scale (i.e. fit in the box)
+ if (scale > 0.0f)
+ {
+ usescale = scale;
+ usewidth = Math.round(scale * width);
+ useheight = Math.round(scale * height);
+ }
+ if (bitmapwidth > 0)
+ {
+ float wscale = (float) bitmapwidth / width;
+ if (wscale > 0.0f && (usescale == 0.0f || wscale < usescale))
+ {
+ usescale = wscale;
+ usewidth = bitmapwidth;
+ useheight = Math.round(usescale * height);
+ }
+ }
+ if (bitmapheight > 0)
+ {
+ float hscale = (float) bitmapheight / height;
+ if (hscale > 0.0f && (usescale == 0.0f || hscale < usescale))
+ {
+ usescale = hscale;
+ usewidth = Math.round(usescale * width);
+ useheight = bitmapheight;
+ }
+ }
+ bi = new BufferedImage(usewidth, useheight, BufferedImage.TYPE_INT_RGB);
graphics = bi.getGraphics();
Graphics2D ig2 = (Graphics2D) graphics;
ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
+ if (usescale > 0.0f)
+ ig2.scale(usescale, usescale);
}
/**
git://source.jalview.org / jalview.git / commitdiff