duplicatesStrategy "INCLUDE"
+ // this mainClassName is mandatory but gets ignored due to manifest created in doFirst{}. Set the Main-Class as an attribute in launcherJar instead
mainClassName = shadow_jar_main_class
mergeServiceFiles()
- classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
+ archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
minimize()
}
- <!-- 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-4195,JAL-4194,JAL-4193 --> sensible responses from the CLI when things go wrong during image export
- Add a command line option to set Jalview properties for this session only
- Add a command line option to suppress opening the startup file for this session
-
-
- JAL-4187 Powershell launcher script fails when given no arguments with the old ArgsParser
-
- known issue ? <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated
-
-
- - <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
- <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
-
- ## Still in progress (delete on release)
-
- - <!-- JAL-2382 --> Import and display sequence-associated contact predictions in CASP-RR format
- - <!-- JAL-2349 --> Contact prediction visualisation
- - <!-- JAL-2348 --> modularise annotation renderer
+ - <!-- JAL-4206 --> Improved file chooser's 'recent files' view and added filter for 'All known alignment files'
+ - <!-- JAL-4206 --> Relative files added to recent files list via import from command line are selected when Jalview opened from same location
+ - <!-- JAL-4308 --> Reduce number of database crossreferences shown in tooltip
+ - <!-- JAL-4315 --> Drag and drop feature colours file on an alignment to quickly apply feature settings
+ - <!-- JAL-3676 --> Improved startup info in console output: which properties file was being used and slight revisions to the formatting of platform information.
+ - <!-- JAL-4304,JAL-4305 --> Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly.
+ - <!-- JAL-1713,JAL-2528 --> Overview display and hidden region visibility stored in Jalview projects
+ - <!-- JAL-4169 --> Updated faq and documentation urls in splashscreen and help documentation
### Development and Deployment
-
+ - <!-- JAL-4054 --> Installers built with install4j10
- <!-- JAL-4167 --> Create separate gradle test task for some tests
- - <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
+ - <!-- JAL-4212 --> Prevent gradle test on macOS continuously grabbing focus
-- <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
++- <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel
+ - <!-- JAL-4288 --> Update .jvl generation in build.gradle for jalview branch builds
- <!-- JAL-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
+ - <!-- JAL-4110 --> Output stderr and stdout when running tests via gradle
+ - <!-- JAL-3599 --> New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress)
-
## Issues Resolved
- <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
- - <!-- JAL-3776 --> Cancelling interactive calculation leaves empty progress bar.
- <!-- JAL-3772 --> Unsaved Alignment windows close without prompting to save, individually or at application quit.
- <!-- JAL-1988 --> Can quit Jalview while 'save project' is in progress
- <!-- JAL-4126 --> 'Use original colours' option of colour by annotation not honoured when restoring view from project
import java.util.Locale;
import java.util.Vector;
+ import javax.swing.AbstractButton;
import javax.swing.ButtonGroup;
-import javax.swing.ButtonModel;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComponent;
import javax.swing.JEditorPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+ import javax.swing.JRadioButtonMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
private static final int MIN_TREE_SELECTION = 3;
private static final int MIN_PCA_SELECTION = 4;
+
+ private String secondaryStructureModelName;
+
+ private void getSecondaryStructureModelName() {
+
+ ScoreModels scoreModels = ScoreModels.getInstance();
+ for (ScoreModelI sm : scoreModels.getModels())
+ {
+ if (sm.isSecondaryStructure())
+ {
+ secondaryStructureModelName = sm.getName();
+ }
+ }
+
+ }
+ private static final int MIN_PASIMAP_SELECTION = 8;
+
AlignFrame af;
JRadioButton pca;
}
};
pca.addActionListener(calcChanged);
+ pasimap.addActionListener(calcChanged); // add the calcChanged ActionListener to pasimap --> <++> idk
neighbourJoining.addActionListener(calcChanged);
averageDistance.addActionListener(calcChanged);
+
+
+ //to do
+ ssSourceDropdown = buildSSSourcesOptionsList();
+ ssSourceDropdown.setVisible(false); // Initially hide the dropdown
/*
* score models drop-down - with added tooltips!
protected void calculate_actionPerformed()
{
boolean doPCA = pca.isSelected();
+ boolean doPaSiMap = pasimap.isSelected();
String modelName = modelNames.getSelectedItem().toString();
- SimilarityParamsI params = getSimilarityParameters(doPCA);
+ String ssSource = "";
+ Object selectedItem = ssSourceDropdown.getSelectedItem();
+ if (selectedItem != null) {
+ ssSource = selectedItem.toString();
+ }
+ SimilarityParams params = getSimilarityParameters(doPCA);
+ if(ssSource.length()>0)
+ {
+ params.setSecondaryStructureSource(ssSource);
+ }
- if (doPCA)
+
+ if (doPCA && !doPaSiMap)
{
openPcaPanel(modelName, params);
}
if (!first)
{
- System.out.println(DASHES);
+ jalview.bin.Console.outPrintln(DASHES);
textarea.append(DASHES);
+ sb.append(DASHES);
}
first = false;
- as.printAlignment(System.out);
+ if (discardAlignments) {
+ as.printAlignment(System.out);
+ }
scores[i][j] = as.getMaxScore() / as.getASeq1().length;
+ alignmentScores[i][j] = as.getAlignmentScore();
totscore = totscore + scores[i][j];
- textarea.append(as.getOutput());
- sequences.add(as.getAlignedSeq1());
- sequences.add(as.getAlignedSeq2());
+ if (suppressTextbox)
+ {
+ textarea.append(as.getOutput());
+ sb.append(as.getOutput());
+ }
+ if (discardAlignments)
+ {
+ sequences.add(as.getAlignedSeq1());
+ sequences.add(as.getAlignedSeq2());
+ }
+
+ firePropertyChange(PROGRESS, progress, ++progress);
}
}
+ alignmentScores[count - 1][count - 1] = Float.NaN;
+
+ this.scores = scores;
+ this.alignmentScores = alignmentScores;
if (count > 2)
{
git://source.jalview.org / jalview.git / commitdiff