jetty-io-9.2.10.v20150310.jar
jetty-server-9.2.10.v20150310.jar
jetty-util-9.2.10.v20150310.jar
-jfreesvg-2.1.jar GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
+jfreesvg-3.4.3.jar GPL v3 licensed library from the JFree suite - last release with Java 1.8 compatibility http://www.jfree.org/jfreesvg/
JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
jhall.jar
Jmol-NO_LOG4J-14.31.53.jar GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile)
regex.jar
saaj.jar
servlet-api-3.1.jar
-slf4j-api-1.7.32.jar MIT license - https://opensource.org/licenses/mit-license.php
+slf4j-api-1.7.36.jar MIT license - https://opensource.org/licenses/mit-license.php - downloaded from https://repo1.maven.org/maven2/org/slf4j/
+slf4j-nop-1.7.36.jar MIT license - https://opensource.org/licenses/mit-license.php - downloaded from https://repo1.maven.org/maven2/org/slf4j/
vamsas-client.jar
VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
wsdl4j.jar
info.events = [ TestLogEvent.FAILED ]
}
+ if (OperatingSystem.current().isMacOsX()) {
+ testTask.systemProperty "apple.awt.UIElement", "true"
+ testTask.environment "JAVA_TOOL_OPTIONS", "-Dapple.awt.UIElement=true"
+ }
ignoreFailures = true // Always try to run all tests for all modules
--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
--- /dev/null
+--open=./examples/test_fab41.result/sample.a2m
+--colour=gecos:flower
+--gui
+--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb
+--paematrix=[label=pAE R1-M3]./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json
+--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb
+--paematrix=[label=pAE R2-M4]./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4_scores.json
+--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb
+--paematrix=[label=pAE R3-M2]./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2_scores.json
+--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5.pdb
+--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=[textrenderer=text]output1.html
-1.8.3-1.2.14_FJVL
+1.8.3-1.3.0_FJVL
-1.8.3-1.2.14_JVL
+1.8.3-1.3.0_JVL
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.14_FJVL</version>
+ <version>1.8.3-1.3.0_FJVL</version>
</parent>
<artifactId>getdown-ant</artifactId>
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.14_FJVL</version>
+ <version>1.8.3-1.3.0_FJVL</version>
</parent>
<artifactId>getdown-core</artifactId>
import java.security.MessageDigest;
+import jalview.util.LaunchUtils;
+
import static com.threerings.getdown.Log.log;
/**
return getJVMPath(appdir, false);
}
+ private static String jvmPath = null;
/**
* Reconstructs the path to the JVM used to launch this process.
*
*/
public static String getJVMPath (File appdir, boolean windebug)
{
- // first look in our application directory for an installed VM
- String vmpath = checkJVMPath(new File(appdir, LOCAL_JAVA_DIR).getAbsolutePath(), windebug);
- if (vmpath == null && isMacOS()) {
- vmpath = checkJVMPath(new File(appdir, LOCAL_JAVA_DIR + "/Contents/Home").getAbsolutePath(), windebug);
+ if (jvmPath != null) {
+ return jvmPath;
}
+
+ // first look in our application directory for an installed VM
+ final String appDir = isMacOS() ?
+ (new File(appdir, LOCAL_JAVA_DIR).getAbsolutePath()) + "/Contents/Home"
+ : new File(appdir, LOCAL_JAVA_DIR).getAbsolutePath();
+
+ String javaBin = LaunchUtils.findJavaBin(appDir, windebug, false);
// then fall back to the VM in which we're already running
- if (vmpath == null) {
- vmpath = checkJVMPath(System.getProperty("java.home"), windebug);
+ if (javaBin == null) {
+ javaBin = LaunchUtils.findJavaBin(System.getProperty("java.home"), windebug, false);
}
// then throw up our hands and hope for the best
- if (vmpath == null) {
+ if (javaBin == null) {
+ javaBin = LaunchUtils.findJavaBin(null, windebug, true);
log.warning("Unable to find java [appdir=" + appdir +
", java.home=" + System.getProperty("java.home") + "]!");
- vmpath = "java";
}
// Oddly, the Mac OS X specific java flag -Xdock:name will only work if java is launched
if (isMacOS()) {
try {
File localVM = new File("/usr/bin/java").getCanonicalFile();
- if (localVM.equals(new File(vmpath).getCanonicalFile())) {
- vmpath = "/usr/bin/java";
+ if (localVM.equals(new File(javaBin).getCanonicalFile())) {
+ javaBin = "/usr/bin/java";
}
} catch (IOException ioe) {
log.warning("Failed to check Mac OS canonical VM path.", ioe);
}
}
- return vmpath;
+ jvmPath = javaBin;
+ return jvmPath;
}
private static String _getMD5FileChecksum (File file) {
public class LaunchUtils
{
+ // setting these is LaunchUtils so don't need to import Platform
+ public final static boolean isMac = System.getProperty("os.name")
+ .indexOf("Mac") > -1;
+
+ public final static boolean isWindows = System.getProperty("os.name")
+ .indexOf("Win") > -1;
+
+ private static boolean isJS = /** @j2sNative true || */
+ false;
+
public static void loadChannelProps(File dir)
{
ChannelProperties.loadProps(dir);
public static int getJavaCompileVersion()
{
- if (JAVA_COMPILE_VERSION > 0)
+ if (LaunchUtils.isJS)
+ {
+ return -1;
+ }
+ else if (JAVA_COMPILE_VERSION > 0)
{
return JAVA_COMPILE_VERSION;
}
public static int getJavaVersion()
{
- if (JAVA_VERSION > 0)
+ if (LaunchUtils.isJS)
+ {
+ return -1;
+ }
+ else if (JAVA_VERSION > 0)
{
return JAVA_VERSION;
}
public static boolean checkJavaVersion()
{
+ if (LaunchUtils.isJS)
+ {
+ return true;
+ }
String buildDetails = "jar:".concat(LaunchUtils.class
.getProtectionDomain().getCodeSource().getLocation().toString()
.concat("!" + "/.build_properties"));
return true;
}
+
+ public static String findJavaBin(boolean winConsole)
+ {
+ return findJavaBin(System.getProperty("java.home"), winConsole, true);
+ }
+
+ /*
+ * Returns a string path to the most likely java binary wanted to run this
+ * installation of Jalview.
+ *
+ * @param winConsole whether to use java.exe (console) in preference to javaw.exe
+ * (only affects Windows).
+ * @param javaHome Try this javaHome dir (defaults to the running java.home).
+ * @param generic Return a generic java command if not found.
+ */
+ public static String findJavaBin(String javaHome, boolean winConsole,
+ boolean generic)
+ {
+ String javaBin = null;
+ final String javaExe = winConsole ? "java.exe" : "javaw.exe";
+ final String java = "java";
+
+ if (javaHome != null)
+ {
+ // property "channel.app_name" is set by install4j when launching getdown
+ String propertyAppName = System.getProperty("channel.app_name");
+ final String appName = (propertyAppName != null
+ && propertyAppName.length() > 0) ? propertyAppName
+ : ChannelProperties.getProperty("app_name");
+
+ final String javaBinDir = javaHome + File.separator + "bin"
+ + File.separator;
+
+ // appName and "Jalview" will not point to javaw.exe or java.exe but in
+ // this case that's okay because the taskbar display name problem doesn't
+ // manifest in Windows. See JAL-3820, JAL-4189.
+ for (String name : new String[] { appName, "Jalview", java, javaExe })
+ {
+ if (LaunchUtils.checkJVMSymlink(javaBinDir + name, winConsole))
+ {
+ javaBin = javaBinDir + name;
+ break;
+ }
+ }
+ }
+
+ if (javaBin == null && generic)
+ {
+ javaBin = LaunchUtils.isWindows ? javaExe : java;
+ }
+
+ return javaBin;
+ }
+
+ /*
+ * checkJVMSymlink returns true if the path in testBin *is* a java binary, or
+ * points to a java binary.
+ * @param testBin The binary or symbolic link to check
+ * @param winConsole whether we are in/want a Windows console (only relevant for Windows,
+ * determines whether we use java.exe or javaw.exe)
+ */
+ private static boolean checkJVMSymlink(String testBin, boolean winConsole)
+ {
+ File testBinFile = new File(testBin);
+ if (!testBinFile.exists())
+ {
+ return false;
+ }
+ File targetFile = null;
+ try
+ {
+ targetFile = testBinFile.getCanonicalFile();
+ } catch (IOException e)
+ {
+ return false;
+ }
+ final String javaExe = winConsole ? "java.exe" : "javaw.exe";
+ if (targetFile != null && ("java".equals(targetFile.getName())
+ || javaExe.equals(targetFile.getName())))
+ {
+ return true;
+ }
+ return false;
+ }
}
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.14_FJVL</version>
+ <version>1.8.3-1.3.0_FJVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
if [ x$JVLVERSION != x ]; then
export VERSION=$JVLVERSION
else
- export VERSION=1.8.3-1.2.14_JVL
+ export VERSION=1.8.3-1.3.0_JVL
fi
if [ x${VERSION%_JVL} = x$VERSION ]; then
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
<packaging>pom</packaging>
- <version>1.8.3-1.2.14_FJVL</version>
+ <version>1.8.3-1.3.0_FJVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
</p>
<p>
- <em>Important!</em> If you use <code>--output</code> or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified <code>--headless</code>). To use Jalview with <code>--output</code> and not assume headless mode, use the <code>--gui</code> or <code>--noheadless</code> argument (the order doesn't matter).
+ <em>Important!</em> If you use <code>--output</code> or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified <code>--headless</code>). To use Jalview with <code>--output</code> and not assume headless mode, use the <code>--gui</code> argument (the order doesn't matter).
</p>
<p>
<tr valign="top"><td><code>‑‑help‑all</code></td><td>Help for all arguments</td></tr>
<tr valign="top">
- <td><code>‑‑headless / ‑‑noheadless</code></td>
- <td>Run Jalview in headless (/ or not in headless) mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
+ <td><code>‑‑headless</code></td>
+ <td>Run Jalview in headless mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
<br/>
- If you use a command line argument to specify an output file of some kind (<code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then <strong>headless mode will be assumed</strong>. If you don't want this behaviour use <code>--noheadless</code> or <code>--gui</code>.
+ If you use a command line argument to specify an output file of some kind (<code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then <strong>headless mode will be assumed</strong>. If you don't want this behaviour use <code>--gui</code>.
</td>
</tr>
<strong>If you specify an argument for an output file</strong> (one or more of <code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then it will be assumed that you wish to <strong>run in headless mode</strong>.
</p>
<p>
- You can force Jalview to run in graphical mode using the <code>--gui</code> or <code>--noheadless</code> arguments.
+ You can force Jalview to run in graphical mode using the <code>--gui</code> argument.
</p>
<p>
### Other improvements
+
+- <!-- JAL-4250 --> Secondary structure annotation glyphs are rendered anti-aliasing when enabled
+- <!-- JAL-325 --> Helix and Sheet glyphs vertically centered with respect to grey coil secondary structure annotation track
+- <!-- JAL-4253 --> Lower line of the sequence group border does not align with vertical and background residue box
+- <!-- JAL-4250 --> Updated JFreeSVG (https://www.jfree.org/jfreesvg) from 2.1 to 3.4.3
- <!-- JAL-3119 --> Name of alignment and view included in overview window's title
- <!-- JAL-4213 --> "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range
- <!-- JAL-4119 --> EMBL-EBI SIFTS file downloads now use split directories
- <!-- JAL-4167 --> Create separate gradle test task for some tests
- <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
+- <!-- JAL-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
## Issues Resolved
- <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
action.cluster_matrix = Cluster matrix
action.clustering_matrix_for = Calculating tree for matrix {0} and clustering at {1}
action.cluster_matrix_tooltip = Computes an average distance tree for the matrix and displays it
-
+label.all_known_alignment_files = All known alignment files
label.nothing_selected = Nada seleccionado
prompt.analytics_title = Jalview Estadísticas de Uso
prompt.analytics = ¿Quiere ayudar a mejorar Jalview habilitando la recopilación de estadísticas de uso con análisis Plausible?\nPuede habilitar o deshabilitar el seguimiento de uso en las preferencias.
+label.all_known_alignment_files = Todos los archivos de alineación conocidos
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;
if (avm == null)
return true;
- /*
- * // 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;
- */
+ // set wrap scope here so it can be applied after structures are opened
+ boolean wrap = false;
+
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
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", "");
false, false);
}
+ // wrap alignment? do this last for formatting reasons
+ wrap = ArgParser.getFromSubValArgOrPref(avm, 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);
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;
- }
- }
- }
+ ViewerType viewerType = ViewerType.getFromString(sViewer);
// TODO use ssFromStructure
StructureViewer sv = StructureChooser
}
}
+ if (wrap)
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ af.setWrapFormat(wrap, true);
+ }
+ }
+
/*
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
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;
seq = al.getSequenceAt(subVals.getIndex());
}
}
- else if (idAv != null)
+ if (seq == null && idAv != null)
{
seq = al.findName(idAv.getValue());
}
*/
package jalview.bin;
-import java.util.Locale;
-
import java.awt.HeadlessException;
+import java.util.Locale;
public class HiDPISetting
{
}
} catch (NumberFormatException e)
{
- jalview.bin.Console.errPrintln(setHiDPIScalePropertyName + " property give ("
- + setHiDPIScaleProperty + ") but not parseable as integer");
+ jalview.bin.Console.errPrintln(setHiDPIScalePropertyName
+ + " property give (" + setHiDPIScaleProperty
+ + ") but not parseable as integer");
}
}
if (setHiDPI && setHiDPIScale > 0)
try
{
int existingPropertyVal = Integer.parseInt(existingProperty);
- jalview.bin.Console.outPrintln("Existing " + scalePropertyName + " is "
- + existingPropertyVal);
+ jalview.bin.Console.outPrintln("Existing " + scalePropertyName
+ + " is " + existingPropertyVal);
if (existingPropertyVal > 1)
{
setHiDPIScale(existingPropertyVal);
}
} catch (NumberFormatException e)
{
- jalview.bin.Console.outPrintln("Could not convert property " + scalePropertyName
- + " vale '" + existingProperty + "' to number");
+ jalview.bin.Console.outPrintln(
+ "Could not convert property " + scalePropertyName
+ + " vale '" + existingProperty + "' to number");
}
}
dpi = screenInfo.getScreenResolution();
} catch (HeadlessException e)
{
- jalview.bin.Console.errPrintln("Cannot get screen resolution: " + e.getMessage());
+ if (isLinux)
+ {
+ jalview.bin.Console.errPrintln(
+ "Cannot get screen resolution: " + e.getMessage());
+ }
}
// try and get screen size height and width
mindimension = Math.min(height, width);
} catch (HeadlessException e)
{
- jalview.bin.Console.errPrintln(
- "Cannot get screen size height and width:" + e.getMessage());
+ if (isLinux)
+ {
+ jalview.bin.Console
+ .errPrintln("Cannot get screen size height and width:"
+ + e.getMessage());
+ }
}
// attempt at a formula for scaling based on screen dpi and mindimension.
UIManager.put("TabbedPane.tabType", "card");
UIManager.put("TabbedPane.showTabSeparators", true);
UIManager.put("TabbedPane.showContentSeparator", true);
- UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
+ // UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
UIManager.put("TabbedPane.tabsOverlapBorder", true);
UIManager.put("TabbedPane.hasFullBorder", true);
UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
{
private final static String startClass = "jalview.bin.Jalview";
- private static boolean checkJVMSymlink(String testBin)
- {
- File testBinFile = new File(testBin);
- if (!testBinFile.exists())
- {
- return false;
- }
- File targetFile = null;
- try
- {
- targetFile = testBinFile.getCanonicalFile();
- } catch (IOException e)
- {
- return false;
- }
- if (targetFile != null && ("java".equals(targetFile.getName())
- || "java.exe".equals(targetFile.getName())))
- {
- return true;
- }
- return false;
- }
+ private final static String headlessProperty = "java.awt.headless";
/**
* main method for jalview.bin.Launcher. This restarts the same JRE's JVM with
{
if (!LaunchUtils.checkJavaVersion())
{
- jalview.bin.Console.errPrintln("WARNING - The Java version being used (Java "
- + LaunchUtils.getJavaVersion()
- + ") may lead to problems. This installation of Jalview should be used with Java "
- + LaunchUtils.getJavaCompileVersion() + ".");
- }
- final String appName = ChannelProperties.getProperty("app_name");
- final String javaBinDir = System.getProperty("java.home")
- + File.separator + "bin" + File.separator;
- String javaBin = null;
- if (javaBin == null && checkJVMSymlink(javaBinDir + appName))
- {
- javaBin = javaBinDir + appName;
- }
- if (javaBin == null && checkJVMSymlink(javaBinDir + "Jalview"))
- {
- javaBin = javaBinDir + "Jalview";
- }
- if (javaBin == null)
- {
- javaBin = "java";
- }
-
- List<String> command = new ArrayList<>();
- command.add(javaBin);
-
- String memSetting = null;
-
- boolean isAMac = System.getProperty("os.name").indexOf("Mac") > -1;
-
- for (String jvmArg : ManagementFactory.getRuntimeMXBean()
- .getInputArguments())
- {
- command.add(jvmArg);
+ jalview.bin.Console
+ .errPrintln("WARNING - The Java version being used (Java "
+ + LaunchUtils.getJavaVersion()
+ + ") may lead to problems. This installation of Jalview should be used with Java "
+ + LaunchUtils.getJavaCompileVersion() + ".");
}
- command.add("-cp");
- command.add(ManagementFactory.getRuntimeMXBean().getClassPath());
String jvmmempc = null;
String jvmmemmax = null;
boolean debug = false;
boolean wait = true;
boolean quiet = false;
+ boolean headless = false;
+ boolean gui = false;
boolean stdout = false;
// must set --debug before --launcher...
boolean launcherstop = false;
{
quiet = true;
}
+ if (arg.equals("--headless"))
+ {
+ headless = true;
+ }
+ if (arg.equals("--gui"))
+ {
+ gui = true;
+ }
if (arg.equals("--output=-")
|| (arg.equals("-") && "--output".equals(previousArg)))
{
arguments.add(arg);
}
}
+ if (gui)
+ {
+ // --gui takes precedence over --headless
+ headless = false;
+ }
+
+ final String appName = ChannelProperties.getProperty("app_name");
+
+ // if we're using jalview.bin.Launcher we always assume a console is in use
+ final String javaBin = LaunchUtils.findJavaBin(true);
+
+ List<String> command = new ArrayList<>();
+ command.add(javaBin);
+
+ String memSetting = null;
+
+ for (String jvmArg : ManagementFactory.getRuntimeMXBean()
+ .getInputArguments())
+ {
+ command.add(jvmArg);
+ }
+ command.add("-cp");
+ command.add(ManagementFactory.getRuntimeMXBean().getClassPath());
// use saved preferences if no cmdline args
boolean useCustomisedSettings = LaunchUtils
boolean memSet = false;
boolean dockIcon = false;
boolean dockName = false;
+ boolean headlessProp = false;
for (int i = 0; i < command.size(); i++)
{
String arg = command.get(i);
{
dockName = true;
}
+ else if (arg.startsWith("-D" + headlessProperty + "="))
+ {
+ headlessProp = true;
+ }
}
if (!memSet)
}
}
- if (isAMac)
+ if (LaunchUtils.isMac)
{
if (!dockIcon)
{
+ appName);
}
}
+ if (headless && !headlessProp)
+ {
+ System.setProperty(headlessProperty, "true");
+ command.add("-D" + headlessProperty + "=true");
+ }
String scalePropertyArg = HiDPISetting.getScalePropertyArg();
if (scalePropertyArg != null)
{
if (e.getMessage().toLowerCase(Locale.ROOT).contains("memory"))
{
- jalview.bin.Console.errPrintln("Caught a memory exception: " + e.getMessage());
+ jalview.bin.Console
+ .errPrintln("Caught a memory exception: " + e.getMessage());
// Probably the "Cannot allocate memory" error, try without the memory
// setting
ArrayList<String> commandNoMem = new ArrayList<>();
Opt.UNARY, Opt.BOOTSTRAP),
HEADLESS(Type.CONFIG,
"Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed. "
- + "Headless mode is assumed if an output file is to be generated, this can be overridden with --noheadless or --gui.",
- Opt.BOOLEAN, Opt.BOOTSTRAP),
+ + "Headless mode is assumed if an output file is to be generated, this can be overridden with --gui.",
+ Opt.UNARY, Opt.BOOTSTRAP),
GUI(Type.CONFIG,
"Do not run Jalview in headless mode. This overrides the assumption of headless mode when an output file is to be generated.",
Opt.UNARY, Opt.BOOTSTRAP),
}
else if (this.contains(Arg.HEADLESS))
{
- // --headless, --noheadless specified => use value
+ // --headless has been specified on the command line => headless
isHeadless = this.getBoolean(Arg.HEADLESS);
}
else if (this.argsHaveOption(Opt.OUTPUTFILE))
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewportI;
+import jalview.bin.Jalview;
import jalview.io.FileFormatI;
import jalview.util.MessageManager;
public static boolean isNeeded(AlignViewportI viewport,
FileFormatI format)
{
- if (viewport.hasHiddenColumns() || viewport.hasHiddenRows()
- || format.isComplexAlignFile())
- {
- return true;
- }
- return false;
+ return !Jalview.getInstance().isHeadlessMode()
+ && (viewport.hasHiddenColumns() || viewport.hasHiddenRows()
+ || format.isComplexAlignFile());
}
/**
closeAllTabs = true;
}
+ Desktop.closeModal(this);
+
try
{
if (alignPanels != null)
featureSettings.close();
featureSettings = null;
}
+
/*
* this will raise an INTERNAL_FRAME_CLOSED event and this method will
* be called recursively, with the frame now in 'closed' state
@Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
- scaleAbove.setVisible(wrapMenuItem.isSelected());
- scaleLeft.setVisible(wrapMenuItem.isSelected());
- scaleRight.setVisible(wrapMenuItem.isSelected());
- viewport.setWrapAlignment(wrapMenuItem.isSelected());
+ setWrapFormat(wrapMenuItem.isSelected(), false);
+ }
+
+ public void setWrapFormat(boolean b, boolean setMenuItem)
+ {
+ scaleAbove.setVisible(b);
+ scaleLeft.setVisible(b);
+ scaleRight.setVisible(b);
+ viewport.setWrapAlignment(b);
alignPanel.updateLayout();
+ if (setMenuItem)
+ {
+ wrapMenuItem.setSelected(b);
+ }
}
@Override
}
JInternalFrame frame = new JInternalFrame();
-
+ frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
Desktop.addInternalFrame(frame, MessageManager
return alignPanel.overviewPanel;
}
JInternalFrame frame = new JInternalFrame();
+ frame.setFrameIcon(null);
final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
showHidden);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
frame.getHeight(), true, true);
- frame.setFrameIcon(null);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
final AlignmentPanel thePanel = this.alignPanel;
else
{
JInternalFrame frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(new PairwiseAlignPanel(viewport));
Desktop.addInternalFrame(frame,
MessageManager.getString("action.pairwise_alignment"), 600,
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactMatrixI;
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultsI;
Dimension r = null;
if (av.getIdWidth() < 0)
{
- int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
- int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
- int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
- r = calculateIdWidth(maxwidth);
+ r = calculateDefaultAlignmentIdWidth();
av.setIdWidth(r.width);
}
else
return r;
}
+ public Dimension calculateDefaultAlignmentIdWidth()
+ {
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
+ int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
+ return calculateIdWidth(-1, false, false);
+ }
+
/**
* Calculate the width of the alignment labels based on the displayed names
* and any bounds on label width set in preferences.
*/
protected Dimension calculateIdWidth(int maxwidth)
{
+ return calculateIdWidth(maxwidth, true, false);
+ }
+
+ public Dimension calculateIdWidth(int maxwidth,
+ boolean includeAnnotations, boolean visibleOnly)
+ {
Container c = new Container();
FontMetrics fm = c.getFontMetrics(
}
// Also check annotation label widths
- i = 0;
-
- if (al.getAlignmentAnnotation() != null)
+ if (includeAnnotations && al.getAlignmentAnnotation() != null)
{
- fm = c.getFontMetrics(getAlabels().getFont());
-
- while (i < al.getAlignmentAnnotation().length)
+ if (Jalview.isHeadlessMode())
{
- String label = al.getAlignmentAnnotation()[i].label;
- int stringWidth = fm.stringWidth(label);
+ AnnotationLabels aal = this.getAlabels();
+ int stringWidth = aal.drawLabels(null, false, idWidth, false, fm);
idWidth = Math.max(idWidth, stringWidth);
- i++;
+ }
+ else
+ {
+ fm = c.getFontMetrics(getAlabels().getFont());
+
+ for (i = 0; i < al.getAlignmentAnnotation().length; i++)
+ {
+ AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+ if (visibleOnly && !aa.visible)
+ {
+ continue;
+ }
+ 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(
- new Dimension(annotationScroller.getWidth(), annotationHeight));
-
Dimension e = idPanel.getSize();
- alabels.setSize(new Dimension(e.width, annotationHeight));
+ int idWidth = e.width;
+ boolean manuallyAdjusted = this.getIdPanel().getIdCanvas()
+ .manuallyAdjusted();
+ annotationScroller.setPreferredSize(new Dimension(
+ manuallyAdjusted ? idWidth : annotationScroller.getWidth(),
+ annotationHeight));
+
+ alabels.setPreferredSize(new Dimension(idWidth, annotationHeight));
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- annotationSpaceFillerHolder.getWidth(), annotationHeight));
+ manuallyAdjusted ? idWidth
+ : annotationSpaceFillerHolder.getWidth(),
+ annotationHeight));
annotationScroller.validate();
annotationScroller.addNotify();
+ ap.validate();
}
/**
boolean wrap = av.getWrapAlignment();
ViewportRanges ranges = av.getRanges();
ranges.setStartSeq(0);
- scalePanelHolder.setVisible(!wrap);
+ // scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
- idwidthAdjuster.setVisible(!wrap);
+ // Allow idPanel width adjustment in wrap mode
+ idwidthAdjuster.setVisible(true);
if (wrap)
{
}
}
- idSpaceFillerPanel1.setVisible(!wrap);
+ // idSpaceFillerPanel1.setVisible(!wrap);
repaint();
}
public void paintComponent(Graphics g)
{
invalidate(); // needed so that the id width adjuster works correctly
-
Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
- idPanelHolder.setPreferredSize(d);
- hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+ int idWidth = d.width;
+
+ // check wrapped alignment as at least 1 residue width
+ if (av.getWrapAlignment())
+ {
+ SeqCanvas sc = this.getSeqPanel().seqCanvas;
+ if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth())
+ {
+ // need to make some adjustments
+ idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth());
+ av.setIdWidth(idWidth);
+ av.getAlignPanel().getIdPanel().getIdCanvas()
+ .setManuallyAdjusted(true);
+
+ validateAnnotationDimensions(false);
+ }
+ }
+
+ idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height));
+ hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
validate(); // needed so that the id width adjuster works correctly
}
int w = getIdPanel().getWidth();
+ w = this.calculateIdWidth(-1, true, true).width;
return (w > 0 ? w : calculateIdWidth().width);
}
- void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) throws ImageOutputException
+ void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
+ throws ImageOutputException
{
makeAlignmentImage(type, file, renderer,
BitmapImageSizing.nullBitmapImageSizing());
final int borderBottomOffset = 5;
AlignmentDimension aDimension = getAlignmentDimension();
+
// todo use a lambda function in place of callback here?
ImageWriterI writer = new ImageWriterI()
{
}
- public void makePNGImageMap(File imgMapFile, String imageName) throws ImageOutputException
+ public void makePNGImageMap(File imgMapFile, String imageName)
+ throws ImageOutputException
{
// /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
} catch (Exception ex)
{
- throw new ImageOutputException("couldn't write ImageMap due to unexpected error",ex);
+ throw new ImageOutputException(
+ "couldn't write ImageMap due to unexpected error", ex);
}
} // /////////END OF IMAGE MAP
{
int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ if (Jalview.isHeadlessMode())
{
seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
- vscroll.getPreferredSize().width
*/
package jalview.gui;
+import java.awt.Canvas;
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentUtils;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
/**
* height in pixels for allowing height adjuster to be active
*/
- private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+ public static int HEIGHT_ADJUSTER_HEIGHT = 10;
private static final Font font = new Font("Arial", Font.PLAIN, 11);
private static final String COPYCONS_SEQ = MessageManager
.getString("label.copy_consensus_sequence");
+ private static final String ADJUST_ANNOTATION_LABELS_WIDTH_PREF = "ADJUST_ANNOTATION_LABELS_WIDTH";
+
private final boolean debugRedraw = false;
private AlignmentPanel ap;
private boolean resizePanel = false;
+ private int annotationIdWidth = -1;
+
+ public static final String RESIZE_MARGINS_MARK_PREF = "RESIZE_MARGINS_MARK";
+
/**
* Creates a new AnnotationLabels object
*
*/
public AnnotationLabels(AlignmentPanel ap)
{
-
this.ap = ap;
av = ap.av;
ToolTipManager.sharedInstance().registerComponent(this);
pop.add(consclipbrd);
}
- addColourOrFilterByOptions(ap,aa[selectedRow],pop);
-
+ addColourOrFilterByOptions(ap, aa[selectedRow], pop);
+
if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP)
{
- addContactMatrixOptions(ap,aa[selectedRow],pop);
- // Set/adjust threshold for grouping ?
- // colour alignment by this [type]
- // select/hide columns by this row
-
- }
+ addContactMatrixOptions(ap, aa[selectedRow], pop);
+ // Set/adjust threshold for grouping ?
+ // colour alignment by this [type]
+ // select/hide columns by this row
+
}
-
+ }
+
pop.show(this, evt.getX(), evt.getY());
}
static void addColourOrFilterByOptions(final AlignmentPanel ap,
- final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+ final AlignmentAnnotation alignmentAnnotation,
+ final JPopupMenu pop)
{
JMenuItem item;
- item = new JMenuItem(MessageManager.getString("label.colour_by_annotation"));
+ item = new JMenuItem(
+ MessageManager.getString("label.colour_by_annotation"));
item.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
- AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,false);
+ AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation,
+ false);
};
});
pop.add(item);
- if (alignmentAnnotation.sequenceRef!=null)
+ if (alignmentAnnotation.sequenceRef != null)
{
- item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")+" ("+MessageManager.getString("label.per_seq")+")");
+ item = new JMenuItem(
+ MessageManager.getString("label.colour_by_annotation") + " ("
+ + MessageManager.getString("label.per_seq") + ")");
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,true);
+ AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation,
+ true);
};
});
pop.add(item);
}
- item = new JMenuItem(MessageManager.getString("action.select_by_annotation"));
+ item = new JMenuItem(
+ MessageManager.getString("action.select_by_annotation"));
item.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
- AnnotationColumnChooser.displayFor(ap.av,ap,alignmentAnnotation);
+ AnnotationColumnChooser.displayFor(ap.av, ap, alignmentAnnotation);
};
});
pop.add(item);
}
+
static void addContactMatrixOptions(final AlignmentPanel ap,
- final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+ final AlignmentAnnotation alignmentAnnotation,
+ final JPopupMenu pop)
{
-
+
final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation);
JMenuItem item;
if (cm != null)
if (cm.hasGroups())
{
- JCheckBoxMenuItem chitem = new JCheckBoxMenuItem(MessageManager.getString("action.show_groups_on_matrix"));
- chitem.setToolTipText(MessageManager.getString("action.show_groups_on_matrix_tooltip"));
- boolean showGroups = alignmentAnnotation.isShowGroupsForContactMatrix();
- final AlignmentAnnotation sel_row=alignmentAnnotation;
+ JCheckBoxMenuItem chitem = new JCheckBoxMenuItem(
+ MessageManager.getString("action.show_groups_on_matrix"));
+ chitem.setToolTipText(MessageManager
+ .getString("action.show_groups_on_matrix_tooltip"));
+ boolean showGroups = alignmentAnnotation
+ .isShowGroupsForContactMatrix();
+ final AlignmentAnnotation sel_row = alignmentAnnotation;
chitem.setState(showGroups);
chitem.addActionListener(new ActionListener()
{
}
if (cm.hasTree())
{
- item = new JMenuItem(MessageManager.getString("action.show_tree_for_matrix"));
- item.setToolTipText(MessageManager.getString("action.show_tree_for_matrix_tooltip"));
+ item = new JMenuItem(
+ MessageManager.getString("action.show_tree_for_matrix"));
+ item.setToolTipText(MessageManager
+ .getString("action.show_tree_for_matrix_tooltip"));
item.addActionListener(new ActionListener()
{
}
else
{
- item = new JMenuItem(MessageManager.getString("action.cluster_matrix"));
- item.setToolTipText(MessageManager.getString("action.cluster_matrix_tooltip"));
+ item = new JMenuItem(
+ MessageManager.getString("action.cluster_matrix"));
+ item.setToolTipText(
+ MessageManager.getString("action.cluster_matrix_tooltip"));
item.addActionListener(new ActionListener()
{
@Override
public void run()
{
final long progBar;
- ap.alignFrame.setProgressBar(MessageManager.formatMessage("action.clustering_matrix_for",cm.getAnnotDescr(),5f), progBar = System.currentTimeMillis());
+ ap.alignFrame.setProgressBar(
+ MessageManager.formatMessage(
+ "action.clustering_matrix_for",
+ cm.getAnnotDescr(), 5f),
+ progBar = System.currentTimeMillis());
cm.setGroupSet(GroupSet.makeGroups(cm, true));
cm.randomlyReColourGroups();
cm.transferGroupColorsTo(alignmentAnnotation);
}
drawComponent(g2, true, width);
-
}
/**
* @param width
* Width for scaling labels
*/
- public void drawComponent(Graphics g, boolean clip, int width)
+ public void drawComponent(Graphics g, boolean clip, int givenWidth)
{
- if (av.getFont().getSize() < 10)
+ int width = givenWidth;
+ IdwidthAdjuster iwa = null;
+ if (ap != null)
{
- g.setFont(font);
+ iwa = ap.idwidthAdjuster;
+ if ((Cache.getDefault(ADJUST_ANNOTATION_LABELS_WIDTH_PREF, true)
+ || Jalview.isHeadlessMode()))
+ {
+ Graphics2D g2d = (Graphics2D) g;
+ Graphics dummy = g2d.create();
+ int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
+ null);
+ dummy.dispose();
+ Dimension d = ap.calculateDefaultAlignmentIdWidth();
+ int alignmentIdWidth = d.width;
+ if (iwa != null && !iwa.manuallyAdjusted())
+ {
+ // If no manual adjustment to ID column with has been made then adjust
+ // width match widest of alignment or annotation id widths
+ boolean allowShrink = Cache.getDefault("ALLOW_SHRINK_ID_WIDTH",
+ false);
+ width = Math.max(alignmentIdWidth, newAnnotationIdWidth);
+ if (clip && width < givenWidth && !allowShrink)
+ {
+ width = givenWidth;
+ }
+ }
+ else if (newAnnotationIdWidth != annotationIdWidth
+ && newAnnotationIdWidth > givenWidth
+ && newAnnotationIdWidth > alignmentIdWidth)
+ {
+ // otherwise if the annotation id width has become larger than the
+ // current id width, increase
+ width = newAnnotationIdWidth;
+ annotationIdWidth = newAnnotationIdWidth;
+ }
+ // set the width if it's changed
+ if (width != ap.av.getIdWidth())
+ {
+ iwa.setWidth(width);
+ }
+ }
}
else
{
- g.setFont(av.getFont());
+ int newAnnotationIdWidth = drawLabels(g, clip, width, false, null);
+ width = Math.max(newAnnotationIdWidth, givenWidth);
+ }
+ drawLabels(g, clip, width, true, null);
+ }
+
+ /**
+ * Render the full set of annotation Labels for the alignment at the given
+ * 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)
+ * @param clip
+ * - true indicates that only current visible area needs to be
+ * rendered
+ * @param width
+ * Width for scaling labels
+ * @param fmetrics
+ * FontMetrics if Graphics object g is null
+ */
+ public int drawLabels(Graphics g0, boolean clip, int width,
+ boolean actuallyDraw, FontMetrics fmetrics)
+ {
+ if (clip)
+ {
+ clip = Cache.getDefault("MOVE_SEQUENCE_ID_WITH_VISIBLE_ANNOTATIONS",
+ true);
+ }
+ Graphics g = null;
+ // create a dummy Graphics object if not drawing and one is supplied
+ if (g0 != null)
+ {
+ if (!actuallyDraw)
+ {
+ Graphics2D g2d = (Graphics2D) g0;
+ g = g2d.create();
+ }
+ else
+ {
+ g = g0;
+ }
}
+ int actualWidth = 0;
+ if (g != null)
+ {
+ if (av.getFont().getSize() < 10)
+ {
+ g.setFont(font);
+ }
+ else
+ {
+ g.setFont(av.getFont());
+ }
+ }
+
+ FontMetrics fm = fmetrics == null ? g.getFontMetrics(g.getFont())
+ : fmetrics;
+ if (actuallyDraw)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+
+ if (!Cache.getDefault(RESIZE_MARGINS_MARK_PREF, false)
+ && !av.getWrapAlignment())
+ {
+ g.setColor(Color.LIGHT_GRAY);
+ g.drawLine(0, HEIGHT_ADJUSTER_HEIGHT / 4, HEIGHT_ADJUSTER_WIDTH / 4,
+ HEIGHT_ADJUSTER_HEIGHT / 4);
+ g.drawLine(0, 3 * HEIGHT_ADJUSTER_HEIGHT / 4,
+ HEIGHT_ADJUSTER_WIDTH / 4, 3 * HEIGHT_ADJUSTER_HEIGHT / 4);
- FontMetrics fm = g.getFontMetrics(g.getFont());
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
+ }
+ }
- g.translate(0, getScrollOffset());
- g.setColor(Color.black);
+ if (actuallyDraw)
+ {
+ g.translate(0, getScrollOffset());
+ g.setColor(Color.black);
+ }
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;
}
}
- g.setColor(Color.black);
-
+ if (actuallyDraw && g != null)
+ {
+ g.setColor(Color.black);
+ }
offset = -aa[i].height / 2;
if (aa[i].hasText)
vertBar = true;
}
}
- x = width - fm.stringWidth(label) - 3;
+
+ int labelWidth = fm.stringWidth(label) + 3;
+ x = width - labelWidth;
if (aa[i].graphGroup > -1)
{
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)
{
if (aa[gg].graphGroup == aa[i].graphGroup)
{
- x = width - fm.stringWidth(aa[gg].label) - 3;
- g.drawString(aa[gg].label, x, y - graphExtras);
-
- if (aa[gg]._linecolour != null)
+ labelWidth = fm.stringWidth(aa[gg].label) + 3;
+ x = width - labelWidth;
+ if (actuallyDraw && g != null)
{
+ g.drawString(aa[gg].label, x, y - graphExtras);
- g.setColor(aa[gg]._linecolour);
- g.drawLine(x, y - graphExtras + 3,
- x + fm.stringWidth(aa[gg].label),
- y - graphExtras + 3);
- }
+ if (aa[gg]._linecolour != null)
+ {
+
+ g.setColor(aa[gg]._linecolour);
+ g.drawLine(x, y - graphExtras + 3,
+ x + fm.stringWidth(aa[gg].label),
+ y - graphExtras + 3);
+ }
- g.setColor(Color.black);
+ g.setColor(Color.black);
+ }
graphExtras += fontHeight + 8;
}
}
}
- g.setFont(baseFont);
+ if (actuallyDraw && g != null)
+ {
+ g.setFont(baseFont);
+ }
fm = baseMetrics;
fontHeight = ofontH;
}
else
{
- if (vertBar)
+ if (actuallyDraw && g != null)
{
- g.drawLine(width - 3, y + offset - fontHeight, width - 3,
- (int) (y - 1.5 * aa[i].height - offset - fontHeight));
- // g.drawLine(20, y + offset, x - 20, y + offset);
+ if (vertBar)
+ {
+ g.drawLine(width - 3, y + offset - fontHeight, width - 3,
+ (int) (y - 1.5 * aa[i].height - offset - fontHeight));
+ // g.drawLine(20, y + offset, x - 20, y + offset);
+ }
+ g.drawString(label, x, y + offset);
}
- g.drawString(label, x, y + offset);
}
lastSeqRef = aa[i].sequenceRef;
+
+ if (labelWidth > actualWidth)
+ {
+ actualWidth = labelWidth;
+ }
}
}
if (!resizePanel && dragEvent != null && aa != null)
{
- g.setColor(Color.lightGray);
- g.drawString(
- (aa[selectedRow].sequenceRef == null ? ""
- : aa[selectedRow].sequenceRef.getName())
- + aa[selectedRow].label,
- dragEvent.getX(), dragEvent.getY() - getScrollOffset());
+ if (actuallyDraw && g != null)
+ {
+ g.setColor(Color.lightGray);
+ g.drawString(
+ (aa[selectedRow].sequenceRef == null ? ""
+ : aa[selectedRow].sequenceRef.getName())
+ + aa[selectedRow].label,
+ dragEvent.getX(), dragEvent.getY() - getScrollOffset());
+ }
}
if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
- g.drawString(MessageManager.getString("label.right_click"), 2, 8);
- g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
- 18);
+ if (actuallyDraw && g != null)
+ {
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
+ }
}
+
+ return actualWidth;
}
public int getScrollOffset()
import java.awt.geom.AffineTransform;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.List;
import java.util.ListIterator;
import java.util.Locale;
+import java.util.Map;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
}
// Thread off a new instance of the file chooser - this reduces the time
- // it
- // takes to open it later on.
+ // it takes to open it later on.
new Thread(new Runnable()
{
@Override
public void run()
{
jalview.bin.Console.debug("Filechooser init thread started.");
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ String fileFormat = FileLoader.getUseDefaultFileFormat()
+ ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+ : null;
JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
fileFormat);
jalview.bin.Console.debug("Filechooser init thread finished.");
@Override
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ String fileFormat = FileLoader.getUseDefaultFileFormat()
+ ? Cache.getProperty("DEFAULT_FILE_FORMAT")
+ : null;
JalviewFileChooser chooser = JalviewFileChooser.forRead(
Cache.getProperty("LAST_DIRECTORY"), fileFormat,
BackupFiles.getEnabled());
}
/**
- * checks if any progress bars are being displayed in any of the windows managed by the desktop
+ * checks if any progress bars are being displayed in any of the windows
+ * managed by the desktop
+ *
* @return
*/
public boolean operationsAreInProgress()
{
JInternalFrame[] frames = getAllFrames();
- for (JInternalFrame frame:frames)
+ for (JInternalFrame frame : frames)
{
if (frame instanceof IProgressIndicator)
{
- if (((IProgressIndicator)frame).operationInProgress())
+ if (((IProgressIndicator) frame).operationInProgress())
{
return true;
}
}
return operationInProgress();
}
+
+ /**
+ * keep track of modal JvOptionPanes open as modal dialogs for AlignFrames.
+ * The way the modal JInternalFrame is made means it cannot be a child of an
+ * AlignFrame, so closing the AlignFrame might leave the modal open :(
+ */
+ private static Map<AlignFrame, JInternalFrame> alignFrameModalMap = new HashMap<>();
+
+ protected static void addModal(AlignFrame af, JInternalFrame jif)
+ {
+ alignFrameModalMap.put(af, jif);
+ }
+
+ protected static void closeModal(AlignFrame af)
+ {
+ if (!alignFrameModalMap.containsKey(af))
+ {
+ return;
+ }
+ JInternalFrame jif = alignFrameModalMap.get(af);
+ if (jif != null)
+ {
+ try
+ {
+ jif.setClosed(true);
+ } catch (PropertyVetoException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ alignFrameModalMap.remove(af);
+ }
+
}
JvOptionPane.frameDialog(panel, title, JvOptionPane.PLAIN_MESSAGE,
options, ok, actions, false);
- */
+ */
}
}
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Dimension;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics;
void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
int startSeq, int pageHeight)
{
+ drawIdsWrapped(g, alignViewport, startSeq, pageHeight, -1);
+ }
+
+ void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
+ int startSeq, int pageHeight, int idWidth)
+ {
int alignmentWidth = alignViewport.getAlignment().getWidth();
final int alheight = alignViewport.getAlignment().getHeight();
if (labels != null && alignViewport.isShowAnnotation())
{
+ int getWidth = getWidth();
+ int thisIdWidth = getWidth;
g.translate(0, ypos + (alheight * charHeight));
- labels.drawComponent(g, getWidth());
+ if (!manuallyAdjusted())
+ {
+ int getAnnotationsIdWidth = labels.drawLabels(g, false, -1, false,
+ null);
+ thisIdWidth = idWidth < 0 ? getAnnotationsIdWidth : idWidth;
+ if (thisIdWidth > getWidth)
+ {
+ this.setPreferredSize(
+ new Dimension(thisIdWidth, this.getHeight()));
+ this.repaint();
+ alignViewport.setIdWidth(thisIdWidth);
+ }
+ }
+ labels.drawComponent(g, false, thisIdWidth);
g.translate(0, -ypos - (alheight * charHeight));
}
repaint();
}
}
+
+ private boolean manuallyAdjusted = false;
+
+ public boolean manuallyAdjusted()
+ {
+ return manuallyAdjusted;
+ }
+
+ public void setManuallyAdjusted(boolean b)
+ {
+ manuallyAdjusted = b;
+ }
}
*/
package jalview.gui;
-import jalview.api.AlignViewportI;
-
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Graphics;
import javax.swing.JPanel;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+
/**
* DOCUMENT ME!
*
return;
}
+ /*
+ * don't allow residue width to be < 1 in wrapped format
+ */
+ if (viewport.getWrapAlignment())
+ {
+ SeqCanvas sc = ap.getSeqPanel().seqCanvas;
+ if (sc != null && sc.getWrappedCanvasWidth(sc.getWidth() - dif) < 1)
+ {
+ return;
+ }
+ }
+
oldX = evt.getX();
/*
return;
}
viewport.setIdWidth(newWidth);
+ ap.validateAnnotationDimensions(false);
+ ap.paintAlignment(true, false);
+
+ ap.getIdPanel().getIdCanvas().setManuallyAdjusted(true);
+ }
+
+ public void setWidth(int newWidth)
+ {
+ if (newWidth < MIN_ID_WIDTH
+ || ap.getIdPanel().getIdCanvas().manuallyAdjusted())
+ {
+ return;
+ }
+ final AlignViewportI viewport = ap.getAlignViewport();
+ viewport.setIdWidth(newWidth);
ap.paintAlignment(true, false);
}
+ public boolean manuallyAdjusted()
+ {
+ return ap.getIdPanel().getIdCanvas().manuallyAdjusted();
+ }
+
@Override
public void mouseMoved(MouseEvent evt)
{
@Override
public void paintComponent(Graphics g)
{
+ int width = getWidth();
+ int height = getHeight();
g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
+ g.fillRect(0, 0, width, height);
+
+ if (!Cache.getDefault(AnnotationLabels.RESIZE_MARGINS_MARK_PREF, false))
+ // && !ap.getAlignViewport().getWrapAlignment()) // now allowing adjustment
+ // in wrap mode
+ {
+ int spacer = Math.max(2, AnnotationLabels.HEIGHT_ADJUSTER_HEIGHT / 4);
+ g.setColor(Color.LIGHT_GRAY);
+ g.drawLine(width - 3 * spacer, 0, width - 3 * spacer, height / 2);
+ g.drawLine(width - spacer, 0, width - spacer, height / 2);
+ }
+
setCursor(Cursor.getPredefinedCursor(Cursor.W_RESIZE_CURSOR));
}
}
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.StringUtils;
import jalview.util.imagemaker.BitmapImageSizing;
/**
}
public void doExport(File file, Component parent, int width, int height,
- String imageSource, String renderer, BitmapImageSizing userBis) throws ImageOutputException
+ String imageSource, String renderer, BitmapImageSizing userBis)
+ throws ImageOutputException
{
final long messageId = System.currentTimeMillis();
setStatus(
{
if (Desktop.instance.isInBatchMode())
{
- // defensive error report - we could wait for user input.. I guess ?
- throw(new ImageOutputException("Need an output file to render to when exporting images in batch mode!"));
+ // defensive error report - we could wait for user input.. I guess ?
+ throw (new ImageOutputException(
+ "Need an output file to render to when exporting images in batch mode!"));
}
JalviewFileChooser chooser = imageType.getFileChooser();
chooser.setFileView(new JalviewFileView());
renderStyle = "Text";
}
AtomicBoolean textSelected = new AtomicBoolean(
- !"Lineart".equals(renderStyle));
- if ((imageType == TYPE.EPS || imageType == TYPE.SVG)
- && LineartOptions.PROMPT_EACH_TIME.equals(renderStyle)
+ !StringUtils.equalsIgnoreCase("lineart", renderStyle));
+ if ((imageType == TYPE.EPS || imageType == TYPE.SVG) && StringUtils
+ .equalsIgnoreCase(LineartOptions.PROMPT_EACH_TIME, renderStyle)
&& !Jalview.isHeadlessMode())
{
final File chosenFile = file;
else
{
/*
- * character rendering not required, or preference already set
- * - just do the export
+ * character rendering not required, or preference already set
+ * or we're in headless mode - just do the export
*/
exportImage(file, !textSelected.get(), width, height, messageId,
userBis);
messageId);
} catch (Exception e)
{
- jalview.bin.Console.error(String.format("Error creating %s file: %s", type,
- e.toString()),e);
+ 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 java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseMotionAdapter;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import javax.swing.JFrame;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.JRootPane;
import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.event.InternalFrameEvent;
if (parentComponent != this
&& !(parentComponent == null && Desktop.instance == null))
{
+ // note the parent goes back to a JRootPane so is probably
+ // Desktop.getDesktop()
JInternalFrame jif = this.createInternalFrame(
parentComponent != null ? parentComponent : Desktop.instance,
title);
+ // connect to the alignFrame using a map in Desktop
+ if (parentComponent instanceof AlignFrame)
+ {
+ Desktop.addModal((AlignFrame) parentComponent, jif);
+ }
jif.setFrameIcon(null);
jif.addInternalFrameListener(new InternalFrameListener()
{
private void internalDialogHandleResponse()
{
- String responseString = (String) this.getValue();
+ Object value = this.getValue();
+ if (value == null
+ || (value instanceof Integer && (Integer) value == -1))
+ {
+ return;
+ }
+ String responseString = value.toString();
int response = ourOptions.indexOf(responseString);
if (!Platform.isJS())
lp.add(modalInterceptor);
f.toFront();
+ // disable the main menu bar if in Linux
+ JMenuBar menubar = null;
+ if (Platform.isLinux())
+ {
+ JRootPane rootpane = Desktop.getDesktop().getRootPane();
+ menubar = rootpane.getJMenuBar();
+ }
+
// We need to explicitly dispatch events when we are blocking the event
// dispatch thread.
EventQueue queue = Toolkit.getDefaultToolkit().getSystemEventQueue();
try
{
+ if (menubar != null)
+ {
+ // don't allow clicks on main menu on linux due to a hanging bug.
+ // see JAL-4214.
+ setMenusEnabled(menubar, false);
+ }
+
while (!f.isClosed())
{
if (EventQueue.isDispatchThread())
// EventQueue.dispatchEvent() directly, because it is
// protected, unfortunately.
if (ev instanceof ActiveEvent)
+ {
((ActiveEvent) ev).dispatch();
- else if (ev.getSource() instanceof Component)
+ }
+ else if (ev instanceof KeyEvent && ((KeyEvent) ev).isControlDown()
+ && menubar != null)
+ {
+ // temporarily enable menus to send Ctrl+? KeyEvents
+ setMenusEnabled(menubar, true);
((Component) ev.getSource()).dispatchEvent(ev);
+ setMenusEnabled(menubar, false);
+ }
else if (ev.getSource() instanceof MenuComponent)
+ {
((MenuComponent) ev.getSource()).dispatchEvent(ev);
+ }
+ else if (ev.getSource() instanceof Component)
+ {
+ ((Component) ev.getSource()).dispatchEvent(ev);
+ }
// Other events are ignored as per spec in
// EventQueue.dispatchEvent
}
// If we get interrupted, then leave the modal state.
} finally
{
+ // re-enable the main menu bar
+ if (menubar != null)
+ {
+ setMenusEnabled(menubar, true);
+ }
+
// Clean up the modal interceptor.
lp.remove(modalInterceptor);
+ // unpaint the frame
+ f.setVisible(false);
+
+ // close the frame
+ try
+ {
+ f.setClosed(true);
+ } catch (PropertyVetoException e)
+ {
+ f.doDefaultCloseAction();
+ }
+
// Remove the internal frame from its parent, so it is no longer
// lurking around and clogging memory.
Container parent = f.getParent();
if (parent != null)
+ {
parent.remove(f);
+ }
}
}
return jvop;
}
+
+ private static void setMenusEnabled(JMenuBar menubar, boolean b)
+ {
+ for (int i = 0; i < menubar.getMenuCount(); i++)
+ {
+ JMenu menu = menubar.getMenu(i);
+ menu.setEnabled(b);
+ }
+ }
+
}
if (Platform.isJS())
{
details = new JInternalFrame();
+ details.setFrameIcon(null);
JPanel panel = new JPanel(new BorderLayout());
panel.setOpaque(true);
panel.setBackground(Color.white);
pane.setBackground(Color.WHITE);
pane.add(textLabel, BorderLayout.NORTH);
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
}
else
return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
}
+ public int getMinimumWrappedCanvasWidth()
+ {
+ int charWidth = av.getCharWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int labelWidth = 0;
+ if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
+ {
+ labelWidth = getLabelWidth(fm);
+ }
+ labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
+ labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
+ return labelWidthEast + labelWidthWest + charWidth;
+ }
+
/**
* Returns a pixel width sufficient to show the largest sequence coordinate
* (end position) in the alignment, calculated as the FontMetrics width of
}
else if (inGroup)
{
- drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
- drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
+ drawVerticals(g, sx, xwidth, visWidth, oldY, bottom);
+ drawHorizontals(g, sx, xwidth, visWidth, top, bottom+1);
// reset top and bottom
top = -1;
if (inGroup)
{
sy = verticalOffset + ((i - startSeq) * charHeight);
- drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
- drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
+ drawVerticals(g, sx, xwidth, visWidth, oldY, bottom);
+ drawHorizontals(g, sx, xwidth, visWidth, top, bottom+1);
}
}
}
});
featureSettingsUI = new JInternalFrame(MessageManager.getString(
"label.sequence_feature_settings_for_CDS_and_Protein"));
+ featureSettingsUI.setFrameIcon(null);
featureSettingsPanels.setOpaque(true);
JPanel dialog = new JPanel();
import jalview.gui.structurechooser.StructureChooserQuerySource;
import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
import jalview.io.DataSourceType;
-import jalview.io.FileFormatException;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.FilterOption;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
-import jalview.ws.dbsources.EBIAlfaFold;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.sifts.SiftsSettings;
sc.mainFrame.dispose();
if (showRefAnnotations)
+ {
showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+ }
return sv;
}
package jalview.gui;
import java.util.ArrayList;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
public enum ViewerType
{
- JMOL, CHIMERA, CHIMERAX, PYMOL
+ JMOL, CHIMERA, CHIMERAX, PYMOL;
+
+ public static ViewerType getFromString(String viewerString)
+ {
+ ViewerType viewerType = null;
+ if (!"none".equals(viewerString))
+ {
+ for (ViewerType v : EnumSet.allOf(ViewerType.class))
+ {
+ String name = v.name().toLowerCase(Locale.ROOT).replaceAll(" ",
+ "");
+ if (viewerString.equals(name))
+ {
+ viewerType = v;
+ break;
+ }
+ }
+ }
+ return viewerType;
+ }
+
};
/**
private File selectedFile;
+ private static boolean useDefaultFileFormat = false;
+
/**
* default constructor always raised errors in GUI dialog boxes
*/
}
this.setShouldBeSaved();
+ // after first file loaded we revert to assuming a default file format
+ useDefaultFileFormat = true;
}
/**
QuitHandler.Message.UNSAVED_ALIGNMENTS);
}
+ public static boolean getUseDefaultFileFormat()
+ {
+ return useDefaultFileFormat;
+ }
+
}
import java.util.Vector;
import javax.swing.BoxLayout;
-import javax.swing.DefaultListCellRenderer;
import javax.swing.JCheckBox;
import javax.swing.JDialog;
import javax.swing.JFileChooser;
+import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.ListCellRenderer;
import javax.swing.SpringLayout;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.border.TitledBorder;
import javax.swing.filechooser.FileFilter;
import javax.swing.plaf.basic.BasicFileChooserUI;
// file filters to fix bug on Mac OSX
setAcceptAllFileFilterUsed(acceptAny);
+ // add a "All known alignment files" option
+ List<String> allExtensions = new ArrayList<>();
+ for (String[] format : formats)
+ {
+ String[] extensions = format[0].split(",");
+ for (String ext : extensions)
+ {
+ if (!allExtensions.contains(ext))
+ {
+ allExtensions.add(ext);
+ }
+ }
+ }
+ allExtensions.sort(null);
+ JalviewFileFilter alljvf = new JalviewFileFilter(
+ allExtensions.toArray(new String[] {}),
+ MessageManager.getString("label.all_known_alignment_files"));
+ alljvf.setExtensionListInDescription(false);
+ addChoosableFileFilter(alljvf);
+
+ if (selected == null)
+ {
+ chosen = alljvf;
+ }
+
for (String[] format : formats)
{
JalviewFileFilter jvf = new JalviewFileFilter(format[0], format[1]);
}
}
+ if (!file.isAbsolute() && file.exists())
+ {
+ file = file.getAbsoluteFile();
+ }
+
setSelectedFile(file);
}
}
}
list = new JList<>(recent);
-
- DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
- dlcr.setHorizontalAlignment(DefaultListCellRenderer.RIGHT);
- list.setCellRenderer(dlcr);
+ list.setCellRenderer(new recentlyOpenedCellRenderer());
list.addMouseListener(new MouseAdapter()
{
}
});
- this.setBorder(new javax.swing.border.TitledBorder(
- MessageManager.getString("label.recently_opened")));
+ TitledBorder recentlyOpenedBorder = new TitledBorder(
+ MessageManager.getString("label.recently_opened"));
+ recentlyOpenedBorder.setTitleFont(
+ recentlyOpenedBorder.getTitleFont().deriveFont(10f));
+ this.setBorder(recentlyOpenedBorder);
final JScrollPane scroller = new JScrollPane(list);
layout.putConstraint(SpringLayout.NORTH, scroller, 5,
SpringLayout.NORTH, this);
- if (Platform.isAMacAndNotJS())
- {
- scroller.setPreferredSize(new Dimension(500, 100));
- }
- else
- {
- scroller.setPreferredSize(new Dimension(530, 200));
- }
-
+ // one size okay for all
+ scroller.setPreferredSize(new Dimension(280, 105));
this.add(scroller);
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
}
+ class recentlyOpenedCellRenderer extends JLabel
+ implements ListCellRenderer<String>
+ {
+ private final static int maxChars = 46;
+
+ private final static String ellipsis = "...";
+
+ @Override
+ public Component getListCellRendererComponent(
+ JList<? extends String> list, String value, int index,
+ boolean isSelected, boolean cellHasFocus)
+ {
+ String filename = value.toString();
+ String displayFilename;
+ if (filename.length() > maxChars)
+ {
+ StringBuilder displayFileSB = new StringBuilder();
+ File file = new File(filename);
+ displayFileSB.append(file.getName());
+ if (file.getParent() != null)
+ {
+ File parent = file;
+ boolean spaceleft = true;
+ while (spaceleft && parent.getParent() != null)
+ {
+ parent = parent.getParentFile();
+ String name = parent.getName();
+ displayFileSB.insert(0, File.separator);
+ if (displayFileSB.length() + name.length() < maxChars - 1)
+ {
+ displayFileSB.insert(0, name);
+ }
+ else
+ {
+ displayFileSB.insert(0, ellipsis);
+ spaceleft = false;
+ }
+ }
+ if (spaceleft && filename.startsWith(File.separator)
+ && !(displayFileSB.charAt(0) == File.separatorChar))
+ {
+ displayFileSB.insert(0, File.separator);
+ }
+ }
+ displayFilename = displayFileSB.toString();
+ }
+ else
+ {
+ displayFilename = filename;
+ }
+ this.setText(displayFilename.toString());
+ this.setToolTipText(filename);
+ if (isSelected)
+ {
+ setBackground(list.getSelectionBackground());
+ setForeground(list.getSelectionForeground());
+ }
+ else
+ {
+ setBackground(list.getBackground());
+ setForeground(list.getForeground());
+ }
+ this.setHorizontalAlignment(SwingConstants.TRAILING);
+ this.setEnabled(list.isEnabled());
+ this.setFont(list.getFont().deriveFont(12f));
+ this.setOpaque(true);
+ return this;
+ }
+
+ }
+
/*
@Override
public JalviewFileChooser setResponseHandler(Object response,
*/
package jalview.io;
-import java.util.Locale;
-
import java.io.File;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.LinkedHashMap;
+import java.util.Locale;
import java.util.Map;
import java.util.StringTokenizer;
while (extensions.hasNext())
{
- fullDescription += (", " + extensions.next());
+ fullDescription += (", ." + extensions.next());
}
}
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;
{
try
{
+ setFrameIcon(null);
// for Web-page embedding using id=align-frame-div
setName("jalview-alignment");
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(
{
}
-
protected void font_actionPerformed(ActionEvent e)
{
}
}
-
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
protected JPanel scalePanelHolder = newJPanel();
- protected JPanel idPanelHolder = newJPanel();
+ public JPanel idPanelHolder = newJPanel();
protected JPanel idSpaceFillerPanel1 = newJPanel();
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.Stroke;
import java.awt.geom.AffineTransform;
import java.awt.image.ImageObserver;
import java.util.BitSet;
import java.util.Hashtable;
+import org.jfree.graphics2d.svg.SVGGraphics2D;
+import org.jibble.epsgraphics.EpsGraphics2D;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.CodingUtils;
import jalview.analysis.Rna;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
private boolean av_ignoreGapsConsensus;
+ private boolean vectorRendition = false;
+
+ private boolean glyphLineDrawn = false;
+
/**
* attributes set from AwtRenderPanelI
*/
* if new annotation with a closing base pair half of the stem,
* display a backward arrow
*/
- g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[]
{ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
3);
* if annotation ending with an opeing base pair half of the stem,
* display a forward arrow
*/
- g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
+ fillPolygon(g, new int[] { x2 - 5, x2 - 5, x2 },
new int[]
{ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
3);
}
}
// draw arrow body
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 7);
}
void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
int iconOffset, int startRes, int column, boolean validRes,
boolean validEnd)
{
- // jalview.bin.Console.outPrintln(nonCanColor);
+ // Console.info(nonCanColor);
- g.setColor(nonCanColor);
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| !dc.equals(row_annotations[column].displayCharacter);
- // jalview.bin.Console.outPrintln("Column "+column+" diff up: "+diffupstream+"
+ // Console.info("Column "+column+" diff up:
+ // "+diffupstream+"
// down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
+ if (diffupstream || diffdownstream)
+ {
+ // draw glyphline under arrow
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
+ g.setColor(nonCanColor);
if (column > 0 && Rna.isClosingParenthesis(dc))
{
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
{
- g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
x1 += 5;
}
// display a forward arrow
if (diffdownstream)
{
- g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
+ fillPolygon(g, new int[] { x2 - 6, x2 - 6, x2 - 1 },
new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
x2 -= 5;
}
}
}
// draw arrow body
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ unsetAntialias(g);
+ fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
// public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
AlignViewportI av, Graphics g, int activeRow, int startRes,
int endRes)
{
+ if (g instanceof EpsGraphics2D || g instanceof SVGGraphics2D)
+ {
+ this.setVectorRendition(true);
+ }
+ Graphics2D g2d = (Graphics2D) g;
+
long stime = System.currentTimeMillis();
boolean usedFaded = false;
// NOTES:
*
* continue; }
*/
+
// first pass sets up state for drawing continuation from left-hand
// column
// of startRes
+
+ // flag used for vector rendition
+ this.glyphLineDrawn = false;
x = (startRes == 0) ? 0 : -1;
while (x < endRes - startRes)
{
: null;
if (x > -1)
{
+ unsetAntialias(g);
if (activeRow == i)
{
g.setColor(Color.red);
{
if (columnSelection.contains(column))
{
- g.fillRect(x * charWidth, y, charWidth, charHeight);
+ fillRect(g, x * charWidth, y, charWidth, charHeight);
}
}
}
if (row.getInvalidStrucPos() > x)
{
g.setColor(Color.orange);
- g.fillRect(x * charWidth, y, charWidth, charHeight);
+ fillRect(g, x * charWidth, y, charWidth, charHeight);
}
else if (row.getInvalidStrucPos() == x)
{
g.setColor(Color.orange.darker());
- g.fillRect(x * charWidth, y, charWidth, charHeight);
+ fillRect(g, x * charWidth, y, charWidth, charHeight);
}
if (validCharWidth && validRes && displayChar != null
&& (displayChar.length() > 0))
{
- Graphics2D gg = ((Graphics2D) g);
+ // Graphics2D gg = (g);
float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
displayChar.length());
if (row_annotations[column].colour == null)
{
- gg.setColor(Color.black);
+ g2d.setColor(Color.black);
}
else
{
- gg.setColor(row_annotations[column].colour);
+ g2d.setColor(row_annotations[column].colour);
}
/*
/*
* translate to drawing position _before_ applying any scaling
*/
- gg.translate(xPos, yPos);
+ g2d.translate(xPos, yPos);
if (scaledToFit)
{
/*
* use a scaling transform to make the label narrower
* (JalviewJS doesn't have Font.deriveFont(AffineTransform))
*/
- gg.transform(
+ g2d.transform(
AffineTransform.getScaleInstance(fmScaling, 1.0));
}
+ setAntialias(g);
if (column == 0 || row.graph > 0)
{
- gg.drawString(displayChar, 0, 0);
+ g2d.drawString(displayChar, 0, 0);
}
else if (row_annotations[column - 1] == null || (labelAllCols
|| !displayChar.equals(
|| (displayChar.length() < 2
&& row_annotations[column].secondaryStructure == ' ')))
{
- gg.drawString(displayChar, 0, 0);
+ g2d.drawString(displayChar, 0, 0);
}
if (scaledToFit)
{
* undo scaling before translating back
* (restoring saved transform does NOT work in JS PDFGraphics!)
*/
- gg.transform(AffineTransform
+ g2d.transform(AffineTransform
.getScaleInstance(1D / fmScaling, 1.0));
}
- gg.translate(-xPos, -yPos);
+ g2d.translate(-xPos, -yPos);
}
}
if (row.hasIcons)
{
// int nb_annot = x - temp;
- // jalview.bin.Console.outPrintln("\t type :"+lastSS+"\t x :"+x+"\t nbre
+ // Console.info("\t type :"+lastSS+"\t x
+ // :"+x+"\t nbre
// annot :"+nb_annot);
switch (lastSS)
{
// temp = x;
break;
default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * charWidth) - lastSSX, 2);
- // temp = x;
+ if (isVectorRendition())
+ {
+ // draw single full width glyphline
+ drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset);
+ // disable more glyph lines
+ this.glyphLineDrawn = true;
+ }
+ else
+ {
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
break;
}
}
case 'y':
case 'Z':
case 'z':
- // jalview.bin.Console.outPrintln(lastSS);
+ // Console.info(lastSS);
Color nonCanColor = getNotCanonicalColor(lastSS);
drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
x, y, iconOffset, startRes, column, validRes, validEnd);
break;
default:
- drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
+ if (isVectorRendition())
+ {
+ // draw single full width glyphline
+ drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset);
+ // disable more glyph lines
+ this.glyphLineDrawn = true;
+ }
+ else
+ {
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
break;
}
}
}
else
{
- jalview.bin.Console.errPrintln(
+ Console.warn(
"rendered with " + renderer.getClass().toString());
}
}
{
if (clipst)
{
- jalview.bin.Console.errPrintln(
- "Start clip at : " + yfrom + " (index " + f_i + ")");
+ Console.warn("Start clip at : " + yfrom + " (index " + f_i + ")");
}
if (clipend)
{
- jalview.bin.Console.errPrintln(
- "End clip at : " + yto + " (index " + f_to + ")");
+ Console.warn("End clip at : " + yto + " (index " + f_to + ")");
}
}
;
- jalview.bin.Console.errPrintln("Annotation Rendering time:"
+ Console.warn("Annotation Rendering time:"
+ (System.currentTimeMillis() - stime));
}
;
// private Color sdNOTCANONICAL_COLOUR;
- void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
- int y, int iconOffset, int startRes, int column, boolean validRes,
- boolean validEnd)
+ void drawGlyphLine(Graphics g, int lastSSX, int x, int y, int iconOffset)
{
+ if (glyphLineDrawn)
+ {
+ // if we've drawn a single long glyphline for an export, don't draw the
+ // bits
+ return;
+ }
+ unsetAntialias(g);
g.setColor(GLYPHLINE_COLOR);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
- g.setColor(SHEET_COLOUR);
-
if (!validEnd || !validRes || row == null || row[column] == null
|| row[column].secondaryStructure != 'E')
{
- g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - 4,
- 7);
- g.fillPolygon(
+ // draw the glyphline underneath
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+
+ g.setColor(SHEET_COLOUR);
+ fillRect(g, lastSSX, y + 4 + iconOffset,
+ (x * charWidth) - lastSSX - 4, 6);
+ fillPolygon(g,
new int[]
- { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
+ { (x * charWidth) - 6, (x * charWidth) - 6,
+ (x * charWidth - 1) },
new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
+ { y + iconOffset + 1, y + 13 + iconOffset,
+ y + 7 + iconOffset },
3);
}
else
{
- g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX,
- 7);
+ g.setColor(SHEET_COLOUR);
+ fillRect(g, lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX,
+ 6);
}
-
}
void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
int y, int iconOffset, int startRes, int column, boolean validRes,
boolean validEnd)
{
- g.setColor(HELIX_COLOUR);
-
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
- if (USE_FILL_ROUND_RECT)
+ if (USE_FILL_ROUND_RECT || isVectorRendition())
{
+ // draw glyph line behind helix (visible in EPS or SVG output)
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+
+ g.setColor(HELIX_COLOUR);
+ setAntialias(g);
int ofs = charWidth / 2;
// Off by 1 offset when drawing rects and ovals
// to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
+ fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - 1, 8, 8, 8);
if (sCol == 0 || row[sCol - 1] == null
|| row[sCol - 1].secondaryStructure != 'H')
{
else
{
// g.setColor(Color.orange);
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
- 0, 0);
+ fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
+ 0);
}
if (!validRes || row[column] == null
|| row[column].secondaryStructure != 'H')
else
{
// g.setColor(Color.magenta);
- g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset,
- x2 - x1 - ofs + 1, 8, 0, 0);
-
+ fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
+ 8, 0, 0);
}
return;
}
- if (sCol == 0 || row[sCol - 1] == null
- || row[sCol - 1].secondaryStructure != 'H')
+ boolean leftEnd = sCol == 0 || row[sCol - 1] == null
+ || row[sCol - 1].secondaryStructure != 'H';
+ boolean rightEnd = !validRes || row[column] == null
+ || row[column].secondaryStructure != 'H';
+
+ if (leftEnd || rightEnd)
+ {
+ drawGlyphLine(g, lastSSX, x, y, iconOffset);
+ }
+ g.setColor(HELIX_COLOUR);
+
+ if (leftEnd)
{
- g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
+ fillArc(g, lastSSX, y + 3 + iconOffset, charWidth, 8, 90, 180);
x1 += charWidth / 2;
}
- if (!validRes || row[column] == null
- || row[column].secondaryStructure != 'H')
+ if (rightEnd)
{
- g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
- 8, 270, 180);
+ fillArc(g, ((x - 1) * charWidth), y + 3 + iconOffset, charWidth, 8,
+ 270, 180);
x2 -= charWidth / 2;
}
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+ fillRect(g, x1, y + 3 + iconOffset, x2 - x1, 8);
}
void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
{
return;
}
+ Stroke roundStroke = new BasicStroke(1, BasicStroke.CAP_ROUND,
+ BasicStroke.JOIN_ROUND);
+ Stroke squareStroke = new BasicStroke(1, BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_MITER);
+ Graphics2D g2d = (Graphics2D) g;
+ Stroke prevStroke = g2d.getStroke();
+ g2d.setStroke(roundStroke);
int x = 0;
}
g.setColor(Color.gray);
- g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
+ drawLine(g, squareStroke, x * charWidth - charWidth, y2,
+ (eRes - sRes) * charWidth, y2);
eRes = Math.min(eRes, aa_annotations.length);
// standalone value
y1 = y - (int) (((aa_annotations[column].value - min) / range)
* graphHeight);
- g.drawLine(x * charWidth + charWidth / 4, y1,
+ drawLine(g, x * charWidth + charWidth / 4, y1,
x * charWidth + 3 * charWidth / 4, y1);
x++;
continue;
y2 = y - (int) (((aa_annotations[column].value - min) / range)
* graphHeight);
- g.drawLine(x * charWidth - charWidth / 2, y1,
+ drawLine(g, (x - 1) * charWidth + charWidth / 2, y1,
x * charWidth + charWidth / 2, y2);
x++;
}
{
g.setColor(_aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
- g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
+ Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ { 5f, 3f }, 0f);
y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
- g2.setStroke(new BasicStroke());
+ drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2);
}
+ g2d.setStroke(prevStroke);
}
@SuppressWarnings("unused")
g.setColor(Color.gray);
- g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+ drawLine(g, x, y2, (eRes - sRes) * charWidth, y2);
int column;
int aaMax = aa_annotations.length - 1;
{
if (y1 - y2 > 0)
{
- g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
+ fillRect(g, x * charWidth, y2, charWidth, y1 - y2);
}
else
{
- g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
+ fillRect(g, x * charWidth, y1, charWidth, y2 - y1);
}
}
// draw profile if available
// lm is not necessary - we can just use fm - could be off by no more
// than 0.5 px
// LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
- // jalview.bin.Console.outPrintln(asc + " " + dec + " " + (asc - lm.getAscent())
+ // Console.info(asc + " " + dec + " " + (asc -
+ // lm.getAscent())
// + " " + (dec - lm.getDescent()));
double asc = fm.getAscent();
if (_aa.threshold != null)
{
g.setColor(_aa.threshold.colour);
- Graphics2D g2 = (Graphics2D) g;
- g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
+ Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ { 5f, 3f }, 0f);
y2 = (int) (y
- ((_aa.threshold.value - min) / range) * _aa.graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
- g2.setStroke(new BasicStroke());
+ drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2);
}
}
{
eRes = Math.min(eRes, aa_annotations.length);
g.setColor(Color.white);
- g.fillRect(0, 0, width, y);
+ fillRect(g, 0, 0, width, y);
g.setColor(new Color(0, 0, 180));
int x = 0, height;
height = y;
}
- g.fillRect(x, y - height, charWidth, height);
+ fillRect(g, x, y - height, charWidth, height);
}
x += charWidth;
}
return new Color(0, 80, 255);
default:
- jalview.bin.Console.outPrintln("This is not a interaction : " + lastss);
+ Console.info("This is not a interaction : " + lastss);
return null;
}
}
+
+ private void fillPolygon(Graphics g, int[] xpoints, int[] ypoints, int n)
+ {
+ setAntialias(g);
+ g.fillPolygon(xpoints, ypoints, n);
+ }
+
+ /*
+ private void fillRect(Graphics g, int a, int b, int c, int d)
+ {
+ fillRect(g, false, a, b, c, d);
+ }*/
+
+ private void fillRect(Graphics g, int a, int b, int c, int d)
+ {
+ unsetAntialias(g);
+ g.fillRect(a, b, c, d);
+ }
+
+ private void fillRoundRect(Graphics g, int a, int b, int c, int d, int e,
+ int f)
+ {
+ setAntialias(g);
+ g.fillRoundRect(a, b, c, d, e, f);
+ }
+
+ private void fillArc(Graphics g, int a, int b, int c, int d, int e, int f)
+ {
+ setAntialias(g);
+ g.fillArc(a, b, c, d, e, f);
+ }
+
+ private void drawLine(Graphics g, Stroke s, int a, int b, int c, int d)
+ {
+ Graphics2D g2d = (Graphics2D) g;
+ Stroke p = g2d.getStroke();
+ g2d.setStroke(s);
+ drawLine(g, a, b, c, d);
+ g2d.setStroke(p);
+ }
+
+ private void drawLine(Graphics g, int a, int b, int c, int d)
+ {
+ setAntialias(g);
+ g.drawLine(a, b, c, d);
+ }
+
+ private void setAntialias(Graphics g)
+ {
+ if (isVectorRendition())
+ {
+ // no need to antialias vector drawings
+ return;
+ }
+ if (Cache.getDefault("ANTI_ALIAS", true))
+ {
+ Graphics2D g2d = (Graphics2D) g;
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+ }
+
+ private void unsetAntialias(Graphics g)
+ {
+ if (isVectorRendition())
+ {
+ // no need to antialias vector drawings
+ return;
+ }
+ Graphics2D g2d = (Graphics2D) g;
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_OFF);
+ }
+
+ public void setVectorRendition(boolean b)
+ {
+ vectorRendition = b;
+ }
+
+ public boolean isVectorRendition()
+ {
+ return vectorRendition;
+ }
}
public class LaunchUtils
{
+ // setting these is LaunchUtils so don't need to import Platform
+ public final static boolean isMac = System.getProperty("os.name")
+ .indexOf("Mac") > -1;
+
+ public final static boolean isWindows = System.getProperty("os.name")
+ .indexOf("Win") > -1;
+
+ private static boolean isJS = /** @j2sNative true || */
+ false;
+
public static void loadChannelProps(File dir)
{
ChannelProperties.loadProps(dir);
public static int getJavaCompileVersion()
{
- if (Platform.isJS())
+ if (LaunchUtils.isJS)
{
return -1;
}
public static int getJavaVersion()
{
- if (Platform.isJS())
+ if (LaunchUtils.isJS)
{
return -1;
}
public static boolean checkJavaVersion()
{
- if (Platform.isJS())
+ if (LaunchUtils.isJS)
{
return true;
}
return true;
}
+
+ public static String findJavaBin(boolean winConsole)
+ {
+ return findJavaBin(System.getProperty("java.home"), winConsole, true);
+ }
+
+ /*
+ * Returns a string path to the most likely java binary wanted to run this
+ * installation of Jalview.
+ *
+ * @param winConsole whether to use java.exe (console) in preference to javaw.exe
+ * (only affects Windows).
+ * @param javaHome Try this javaHome dir (defaults to the running java.home).
+ * @param generic Return a generic java command if not found.
+ */
+ public static String findJavaBin(String javaHome, boolean winConsole,
+ boolean generic)
+ {
+ String javaBin = null;
+ final String javaExe = winConsole ? "java.exe" : "javaw.exe";
+ final String java = "java";
+
+ if (javaHome != null)
+ {
+ // property "channel.app_name" is set by install4j when launching getdown
+ String propertyAppName = System.getProperty("channel.app_name");
+ final String appName = (propertyAppName != null
+ && propertyAppName.length() > 0) ? propertyAppName
+ : ChannelProperties.getProperty("app_name");
+
+ final String javaBinDir = javaHome + File.separator + "bin"
+ + File.separator;
+
+ // appName and "Jalview" will not point to javaw.exe or java.exe but in
+ // this case that's okay because the taskbar display name problem doesn't
+ // manifest in Windows. See JAL-3820, JAL-4189.
+ for (String name : new String[] { appName, "Jalview", java, javaExe })
+ {
+ if (LaunchUtils.checkJVMSymlink(javaBinDir + name, winConsole))
+ {
+ javaBin = javaBinDir + name;
+ break;
+ }
+ }
+ }
+
+ if (javaBin == null && generic)
+ {
+ javaBin = LaunchUtils.isWindows ? javaExe : java;
+ }
+
+ return javaBin;
+ }
+
+ /*
+ * checkJVMSymlink returns true if the path in testBin *is* a java binary, or
+ * points to a java binary.
+ * @param testBin The binary or symbolic link to check
+ * @param winConsole whether we are in/want a Windows console (only relevant for Windows,
+ * determines whether we use java.exe or javaw.exe)
+ */
+ private static boolean checkJVMSymlink(String testBin, boolean winConsole)
+ {
+ File testBinFile = new File(testBin);
+ if (!testBinFile.exists())
+ {
+ return false;
+ }
+ File targetFile = null;
+ try
+ {
+ targetFile = testBinFile.getCanonicalFile();
+ } catch (IOException e)
+ {
+ return false;
+ }
+ final String javaExe = winConsole ? "java.exe" : "javaw.exe";
+ if (targetFile != null && ("java".equals(targetFile.getName())
+ || javaExe.equals(targetFile.getName())))
+ {
+ return true;
+ }
+ return false;
+ }
}
return min < text.length() + 1 ? min : -1;
}
+ public static boolean equalsIgnoreCase(String s1, String s2)
+ {
+ if (s1 == null || s2 == null)
+ {
+ return s1 == s2;
+ }
+ return s1.toLowerCase(Locale.ROOT).equals(s2.toLowerCase(Locale.ROOT));
+ }
+
public static int indexOfFirstWhitespace(String text)
{
int index = -1;
*/
package jalview.viewmodel.styles;
-import jalview.api.ViewStyleI;
-
import java.awt.Color;
+import jalview.api.ViewStyleI;
+
/**
* A container for holding alignment view properties. View properties are
* data-independent, which means they can be safely copied between views
--- /dev/null
+>101
+P.I...A..Q..I.....H.....I........L.......E........G.......R.......S....D.......E.......Q.....K....E.
+T..LI....RE...V.S.E...A...I......S.......R...S.......L........D....A.....P......L...................
+..........T......S.......V.......R......V...I....I.......T......E.....M........A....K.........G.....
+.H..........F..........G........I..........G........G......E........L....A...SK
+>UPI
+P.Hye.V..S..V.....T.....M........P.......T........G.......Wl......N....T.......V.......R.....K....Q.
+G..MI....DA...V.T.R...A...L......L.......E...A.......I........A....T.....P......F...................
+..........D......Essrfr..V.......R......C...L....I.......P......E.....I........P....D.........G.....
+.N..........W..........G........S..........G........Gya....L........P....L...S-
+>SRR
+P.H...V..A..V.....K.....L........Y.......P........G.......R.......T....E.......Q.......Q.....K....E.
+Q..LA....RA...I.A.D...D...V......M.......R...I.......L........G....S.....S......E...................
+..........A......S.......V.......S......V...S....I.......E......E.....V........D....A.........A.....
+.D..........W..........A........EkvyrplivegG........G......T........L....Y...KK
+>SRR
+P.H...V..I..V.....K.....L........W.......P........G.......R.......S....E.......P.......Q.....K....Q.
+K..LV....ES...V.T.K...A...V......T.......T...S.......L........G....Y.....S......D...................
+..........E......A.......V.......S......V...S....L.......Q......E.....V........P....S.........D.....
+.Q..........WtekvyrpdilG........T..........A........G......R........L....Y...KK
+>MGY
+P.I...V..R..I.....T.....M........F.......E........G.......R.......T....K.......E.......Q.....K....Q.
+E..LA....RV...I.T.E...A...V......V.......N...I.......A........K....T.....T......P...................
+..........D......A.......T.......E......VkdqI....L.......Q......K.....VllvrslrlP....PppasrrqvsG.....
+.A..........W..........S........A..........D........G......K........P....T...SE
+>446
+P.H...V..I..V.....K.....L........W.......P........G.......K.......S....E.......R.......E.....E....T.
+Q..LA....EA...I.T.K...S...V......T.......E...T.......L........N....F.....G......P...................
+..........E......S.......V.......S......V...A....F.......E......E.....I........P....A.........K.....
+.D..........W..........AskvyhadiI..........Gne......G......K........L....Y...KK
+>SRR
+P.L...V..R..I.....T.....Y........P.......R........Ga......L.......S....P.......E.......H.....K....T.
+R..IA....RA...L.T.E...I...V......L.......D...Vevdaa..T........D....A.....G......R...................
+..........M......V.......T.......V......V...H....F.......N......E.....A........A....P.........D.....
+.D..........W..........A........V..........G........G......Eirs.....T....A...AE
+>SRR
+P.L...V..R..I.....T.....Y........P.......R........Ga......L.......S....P.......D.......H.....K....R.
+R..IA....RE...L.T.E...I...V......L.......D...Vevdaa..T........D....A.....G......R...................
+..........M......V.......T.......V......I...H....F.......N......E.....A........A....A.........D.....
+.D..........W..........A........V..........G........G......Eirs.....T....A...AE
+>SRR
+P.R...Y..R..Vip...T.....V........P.......E........G.......Qy......S....N.......E.......S.....R....K.
+A..LV....KD...V.T.E...A...V......V.......R...A.......D........G....G.....K......Y...................
+..........E......Dvapr...V.......W......V...F....P.......T......E.....I........P....D.........G.....
+.Q..........W..........G........S..........R........Gvi....R........P....L...PE
+>SRR
+P.R...Y..R..Iip...T.....V........P.......E........G.......Qy......S....N.......E.......S.....R....K.
+A..LV....KD...V.T.E...A...V......V.......R...A.......D........G....G.....K......Y...................
+..........E......Dvapr...V.......W......V...F....P.......T......E.....I........P....D.........G.....
+.Q..........W..........G........S..........R........Gvi....R........P....L...PE
+>SRR
+P.V...I..E..M.....F.....V........P.......E........G.......La......D....A.......E.......A.....K....R.
+A..LH....DR...V.S.R...Q...V......L.......E...V.......E........G....AtydesP......L...................
+..........A......Qsi.....T.......W......M...L....I.......Q......E.....V........L....E.........C.....
+.G..........W..........S........V..........G........S......K........Avw..A...SE
+>SRR
+P.I...I..E..M.....H.....V........Q.......E........Gv......L.......D....E.......E.......T.....K....R.
+T..LH....ER...V.G.R...Q...V......L.......E...I.......E........G....Any...D......E...................
+..........N......D.......Varllt..F......M...F....I.......R......E.....H........P....E.........G.....
+.G..........F..........S........I..........G........G......E........M....It..SE
+>SRR
+P.Lyr.V..D..V.....T.....V........P.......E........Gsmihg..Q.......G....Pwal....S.......R.....R....R.
+A..IV....RE...V.T.E...I...V......L.......E...A.......E........G....S.....D......P...................
+..........Slgeaw.R.......V.......W......V...V....L.......R......E.....V........G....D.........A.....
+.F..........W..........G........A..........A........G......E........L....-...--
+>SRR
+P.Lyr.V..Q..I.....T.....V........P.......E........Gsmlhg..Q.......G....Pwai....E.......R.....R....R.
+E..LV....RA...V.S.K...A...V......L.......D...A.......E........G....Teyn..P......A...................
+..........Saw....R.......V.......W......V...L....M.......S......E.....I........S....E.........T.....
+.H..........W..........G........A..........A........G......E........-....-...--
+>SRR
+P.L...V..E..M.....S.....F........P.......V........Gv......L.......T....L.......D.......Q.....K....A.
+A..MI....KS...V.T.D...V...V......R.......G...A.......M........K....L.....P......P...................
+..........Dpar...K.......L.......F......V...E....I.......F......E.....T........P....G.........G.....
+.G..........F..........G........Vtakvvvvp..G........Gky....R........P....A...P-
+>SRR
+P.L...V..E..I.....D.....L........L.......E........A.......W.......A....P.......D.......Q.....I....D.
+A..IA....DA...I.H.E...A...M......V.......E...T.......L........G....V.....P......Eraagrdsatkqhfysrfaa
+llaeratvqsA......D.......L.......T......A...V....L.......V......E.....N........S....R.........D.....
+.D..........W..........S........F..........Gm.......G......Q........-....-...--
--- /dev/null
+--nonews
+--nosplash
+--open=./test/files/annotation_label_width/sample.a2m
+--colour=gecos:flower
+--gui
+--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb
+--paematrix=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json
+--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb
+--paematrix=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4_scores.json
+--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb
+--paematrix=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2_scores.json
+--structure=[structureviewer=none]./examples/test_fab41.result/test_fab41_unrelaxed_rank_4_model_5.pdb
+--paematrix=./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=./examples/test_fab41.result/test_fab41_unrelaxed_rank_5_model_1_scores.json
--- /dev/null
+/*
+ * 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.gui;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import java.io.File;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.structure.StructureImportSettings.TFType;
+
+public class AnnotationLabelsTest2
+{
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ setUpJvOptionPane();
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "--nonews", "--nosplash", });
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ /**
+ * configure (read-only) properties for test to ensure Consensus is computed
+ * for colour Above PID testing
+ */
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.TRUE.toString());
+
+ }
+
+ public static void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(
+ groups =
+ { "Functional", "testTask1" },
+ dataProvider = "openFilesWithIdWidthChanges")
+ public void testIdWidthChanges(String alignmentFilename, boolean wrap,
+ int idWidth1min, int idWidth1max, int manualWidth,
+ String structureFilename, String paeFilename,
+ boolean secondaryStructureView, TFType temperatureFactorType,
+ ViewerType viewerType, int idWidth2min, int idWidth2max)
+ {
+ AlignFrame af = new FileLoader()
+ .LoadFileWaitTillLoaded(alignmentFilename, DataSourceType.FILE);
+ try
+ {
+ Thread.sleep(200); // to allow alignment annotations to open
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ AlignViewport av = af.getCurrentView();
+
+ int idWidth = 0;
+
+ idWidth = av.getIdWidth();
+ assertTrue(idWidth > idWidth1min,
+ "idWidth (" + idWidth + ") is not greater than " + idWidth1min);
+ assertTrue(idWidth < idWidth1max,
+ "idWidth (" + idWidth + ") is not narrower than" + idWidth1max);
+
+ // set wrap
+ if (wrap)
+ {
+ af.setWrapFormat(true, false);
+ idWidth = av.getIdWidth();
+ assertTrue(idWidth > idWidth1min, "After wrap idWidth (" + idWidth
+ + ") is not greater than " + idWidth1min);
+ assertTrue(idWidth < idWidth1max, "After wrap idWidth (" + idWidth
+ + ") is not narrower than" + idWidth1max);
+ }
+
+ AlignmentI al = av.getAlignment();
+ SequenceI s = al.getSequenceAt(0);
+ AlignmentPanel ap = af.alignPanel;
+
+ File structureFile = new File(structureFilename);
+ File paeFile = new File(paeFilename);
+
+ StructureViewer sv = StructureChooser.openStructureFileForSequence(null,
+ null, ap, s, false, structureFile.getAbsolutePath(),
+ temperatureFactorType, paeFile.getAbsolutePath(), true,
+ secondaryStructureView, false, viewerType);
+ // give time for annotations to open
+ try
+ {
+ Thread.sleep(200); // to allow alignment annotations to open
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ // idWidth = ap.getIdPanel().getWidth();
+ idWidth = av.getIdWidth();
+ assertTrue(idWidth > idWidth2min,
+ "idWidth (" + idWidth + ") is not greater than " + idWidth2min);
+ assertTrue(idWidth < idWidth2max,
+ "idWidth (" + idWidth + ") is not narrower than" + idWidth2max);
+ }
+
+ @Test(
+ groups =
+ { "Functional", "testTask1" },
+ dataProvider = "openFilesWithIdWidthChanges")
+ public void testIdWidthNoChanges(String alignmentFilename, boolean wrap,
+ int idWidth1min, int idWidth1max, int manualWidth,
+ String structureFilename, String paeFilename,
+ boolean secondaryStructureView, TFType temperatureFactorType,
+ ViewerType viewerType, int idWidth2min, int idWidth2max)
+ {
+ AlignFrame af = new FileLoader()
+ .LoadFileWaitTillLoaded(alignmentFilename, DataSourceType.FILE);
+ try
+ {
+ Thread.sleep(200); // to allow alignment annotations to open
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ AlignViewport av = af.getCurrentView();
+
+ int idWidth = 0;
+
+ idWidth = av.getIdWidth();
+ assertTrue(idWidth > idWidth1min,
+ "idWidth (" + idWidth + ") is not greater than " + idWidth1min);
+ assertTrue(idWidth < idWidth1max,
+ "idWidth (" + idWidth + ") is not narrower than" + idWidth1max);
+
+ AlignmentI al = av.getAlignment();
+ SequenceI s = al.getSequenceAt(0);
+ AlignmentPanel ap = af.alignPanel;
+
+ // set width manually
+ av.setIdWidth(manualWidth);
+ ap.validateAnnotationDimensions(false);
+ ap.paintAlignment(true, false);
+ ap.getIdPanel().getIdCanvas().setManuallyAdjusted(true);
+
+ idWidth = av.getIdWidth();
+ assertEquals(idWidth, manualWidth,
+ "idWidth is not set to the manually set width " + manualWidth);
+
+ File structureFile = new File(structureFilename);
+ File paeFile = new File(paeFilename);
+
+ StructureViewer sv = StructureChooser.openStructureFileForSequence(null,
+ null, ap, s, false, structureFile.getAbsolutePath(),
+ temperatureFactorType, paeFile.getAbsolutePath(), false,
+ secondaryStructureView, false, viewerType);
+
+ idWidth = ap.getIdPanel().getWidth();// av.getIdWidth();
+ idWidth = av.getIdWidth();
+ assertEquals(idWidth, manualWidth,
+ "idWidth is not set to the manually set width " + manualWidth
+ + " after adding structure annotations");
+ assertFalse(idWidth > idWidth2min,
+ "idWidth (" + idWidth + ") is greater than " + idWidth2min);
+ }
+
+ @DataProvider(name = "openFilesWithIdWidthChanges")
+ public Object[][] openFilesWithIdWidthChanges()
+ {
+ /*
+ String alignmentFilename,
+ boolean wrap,
+ int idWidth1min,
+ int idWidth1max,
+ int manualWidth, // ignored by testIdWidthChanges()
+ String structureFilename,
+ String paeFilename,
+ boolean secondaryStructureView,
+ TFType temperatureFactorType,
+ ViewerType viewerType,
+ int idWidth2min,
+ int idWidth2max,
+ */
+ return new Object[][] {
+ //
+ /*
+ */
+ { "./test/files/annotation_label_width/sample.a2m", false, 50, 70,
+ 100,
+ "./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
+ "./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json",
+ true, TFType.PLDDT, null, 115, 130 },
+ { "./test/files/annotation_label_width/sample.a2m", true, 50, 70,
+ 100,
+ "./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb",
+ "./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json",
+ true, TFType.PLDDT, null, 115, 130 },
+ /*
+ */
+ };
+ }
+
+}
--- /dev/null
+#!/usr/bin/env bash
+
+###############################
+# Wrapper for Jalview
+#
+# 2023-08-16 Jalview 2.11.3.0 has new command line arguments
+# Old command line arguments are currently detected and actioned
+# but are no longer supported and will be removed at a later date.
+#
+# See
+# Jalview -> Help -> Documentation -> Command Line -> introduction and reference
+# or
+# https://www.jalview.org/help/html/features/clarguments.html
+# for details of the new command line arguments.
+#
+# Note, in order to run commandline-only calls use
+# --headless
+#
+# By default, this wrapper executes java -version to determine the JRE version
+# Set JALVIEW_JRE=j1.8 or JALVIEW_JRE=j11 to skip the version check.
+#
+# By default, this wrapper does NOT restrict the memory consumption of Jalview.
+# Set eg. JALVIEW_MAXMEM=1g to set the maximal memory of Jalview's VM
+#
+# This script is maintained in the Jalview repository in utils/conda/jalview.sh
+###############################
+
+declare -a ARGS=("${@}")
+ARG1=$1
+
+# this function is because there's no readlink -f in Darwin/macOS
+function readlinkf() {
+ FINDFILE="$1"
+ FILE="${FINDFILE}"
+ PREVFILE=""
+ C=0
+ MAX=100 # just in case we end up in a loop
+ FOUND=0
+ while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
+ PREVFILE="${FILE}"
+ FILE="$(readlink "${FILE}")"
+ if [ -z "${FILE}" ]; then
+ # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
+ FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
+ FOUND=1
+ elif [ "${FILE#/}" = "${FILE}" ]; then
+ # FILE is not an absolute path link, we need to add the relative path to the previous dir
+ FILE="$(dirname "${PREVFILE}")/${FILE}"
+ fi
+ C=$((C+1))
+ done
+ if [ "${FOUND}" -ne 1 ]; then
+ echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
+ exit 1
+ fi
+ echo "${FILE}"
+}
+
+ISMACOS=0
+if [ "$( uname -s )" = "Darwin" ]; then
+ ISMACOS=1
+fi
+
+# check for headless mode
+HEADLESS=0
+GUI=0
+HELP=0
+DEBUG=0
+for RAWARG in "${@}"; do
+ ARG="${RAWARG%%=*}"
+ case "${ARG}" in
+ --headless|--output|--image|--structureimage)
+ HEADLESS=1
+ ;;
+ --help|--help-*|--version)
+ HELP=1
+ ;;
+ --gui)
+ GUI=1
+ ;;
+ --debug)
+ DEBUG=1
+ ;;
+ esac
+
+ if [ "${HELP}" = 1 ]; then
+ # --help takes precedence
+ HEADLESS=1
+ GUI=0
+ elif [ "${GUI}" = 1 ]; then
+ # --gui takes precedence over --headless
+ HEADLESS=0
+ fi
+done
+
+declare -a JVMARGS=()
+
+# set vars for being inside the macos App Bundle
+if [ "${ISMACOS}" = 1 ]; then
+# MACOS ONLY
+ DIR="$(dirname "$(readlinkf "$0")")"
+ JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${DIR}/jalview_logo.png" )
+else
+# NOT MACOS
+ DIR="$(dirname "$(readlink -f "$0")")"
+fi
+
+if [ "${HEADLESS}" = 1 ]; then
+ # this suppresses the Java icon appearing in the macOS Dock and maybe other things in other OSes
+ JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
+fi
+
+JAVA=java
+
+# decide which jalview jar to launch - either 'j11' or 'j1.8'
+if [[ "$JALVIEW_JRE" != "j11" && "$JALVIEW_JRE" != "j1.8" ]]; then
+ JALVIEW_JRE="j11"
+ # if java 8 is installed we pick the j1.8 build
+ if [[ $( "${JAVA}" -version 2>&1 | grep '"1.8' ) != "" ]]; then
+ JALVIEW_JRE="j1.8"
+ fi
+fi
+
+JARPATH="${DIR}/jalview-all-${JALVIEW_JRE}.jar"
+
+# check if memory maximum is set and if so forward to java-based jalview call
+if [ \! -z "$JALVIEW_MAXMEM" ]; then
+ JVMARGS=( "${JVMARGS[@]}" "-Xmx${JALVIEW_MAXMEM}" )
+fi
+
+# WINDOWS ONLY (Cygwin or WSL)
+# change paths for Cygwin or Windows Subsystem for Linux (WSL)
+if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
+ if [ "$(uname -o)" = "Cygwin" ]; then
+ # CYGWIN
+ JARPATH="$(cygpath -pw "${JARPATH}")"
+ # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
+ ARGS=()
+ for ARG in "${@}"; do
+ if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
+ ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
+ else
+ ARGS=( "${ARGS[@]}" "${ARG}" )
+ fi
+ done
+ elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
+ # WSL
+ JARPATH="$(wslpath -aw "${JARPATH}")"
+ ARGS=()
+ for ARG in "${@}"; do
+ if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
+ # annoyingly wslpath does not work if the file doesn't exist!
+ ARGBASENAME="$(basename "${ARG}")"
+ ARGDIRNAME="$(dirname "${ARG}")"
+ ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
+ else
+ ARGS=( "${ARGS[@]}" "${ARG}" )
+ fi
+ done
+ JAVA="${JAVA}.exe"
+ fi
+fi
+
+# get console width -- three ways to try, just in case
+if command -v tput 2>&1 >/dev/null; then
+ COLUMNS=$(tput cols) 2>/dev/null
+elif command -v stty 2>&1 >/dev/null; then
+ COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
+elif command -v resize 2>&1 >/dev/null; then
+ COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
+fi
+JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
+
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: "${JAVA}" "${JVMARGS[@]}" -jar \""${JARPATH}"\" "${ARGS[@]}"
+fi
+
+"${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" "${ARGS[@]}"
ISMACOS=1
fi
+# check for headless mode
+HEADLESS=0
+GUI=0
+HELP=0
+DEBUG=0
+for RAWARG in "${@}"; do
+ ARG="${RAWARG%%=*}"
+ case "${ARG}" in
+ --headless|--output|--image|--structureimage)
+ HEADLESS=1
+ ;;
+ --help|--help-*|--version|-h)
+ HELP=1
+ ;;
+ --gui)
+ GUI=1
+ ;;
+ --debug)
+ DEBUG=1
+ ;;
+ esac
+
+ if [ "${HELP}" = 1 ]; then
+ # --help takes precedence
+ HEADLESS=1
+ GUI=0
+ elif [ "${GUI}" = 1 ]; then
+ # --gui takes precedence over --headless
+ HEADLESS=0
+ fi
+done
+
declare -a JVMARGS=()
# set vars for being inside the macos App Bundle
if [ "${ISMACOS}" = 1 ]; then
# MACOS ONLY
DIR="$(dirname "$(readlinkf "$0")")"
- APP="${DIR%.app/Contents/*}".app
- if [ "${APP}" = "${APP%.app}" ]; then
- echo "Could not find Jalview.app" >&2
- exit 2
- fi
- APPDIR="${APP}/Contents/Resources/app"
+ APPDIR="${DIR%/bin}"
JAVA="${APPDIR}/jre/Contents/Home/bin/java"
JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
else
JAVA="${APPDIR}/jre/bin/java"
fi
+if [ "${HEADLESS}" = 1 ]; then
+ # this suppresses the Java icon appearing in the macOS Dock and maybe other things in other OSes
+ JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
+fi
+
SYSJAVA=java
GETDOWNTXT="${APPDIR}/getdown.txt"
echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
fi
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" \""${JVMARGS[@]}"\" -cp \""${CLASSPATH}"\" jalview.bin.Launcher "${ARGS[@]}"
+fi
+
"${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher "${ARGS[@]}"
git://source.jalview.org / jalview.git / commitdiff
