From: Jim Procter Date: Thu, 16 May 2024 07:07:17 +0000 (+0100) Subject: Merge branch 'develop' into feature/JAL-4159_pasimap X-Git-Tag: Release_2_11_4_0~31^2~18^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=37c507c5ed74c4b1564556a19d0bc651f8dccc2d;p=jalview.git Merge branch 'develop' into feature/JAL-4159_pasimap doesn't seem to have apache-math present Conflicts: build.gradle --- 37c507c5ed74c4b1564556a19d0bc651f8dccc2d diff --cc build.gradle index 800fe42,6df3ec9..90686b3 --- a/build.gradle +++ b/build.gradle @@@ -2157,9 -2204,10 +2222,10 @@@ shadowJar 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() } diff --cc help/markdown/releases/release-2_11_3_0.md index 206bbba,c732130..dab5393 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@@ -51,35 -58,29 +58,28 @@@ channel: "release - Name of alignment and view included in overview window's title - "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range - EMBL-EBI SIFTS file downloads now use split directories - - - 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 ? 'Reload' for a jalview project results in all windows being duplicated - - - - Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers) - In Linux desktops' task-managers, the grouped Jalview windows get a generic name - - ## Still in progress (delete on release) - - - Import and display sequence-associated contact predictions in CASP-RR format - - Contact prediction visualisation - - modularise annotation renderer + - Improved file chooser's 'recent files' view and added filter for 'All known alignment files' + - Relative files added to recent files list via import from command line are selected when Jalview opened from same location + - Reduce number of database crossreferences shown in tooltip + - Drag and drop feature colours file on an alignment to quickly apply feature settings + - Improved startup info in console output: which properties file was being used and slight revisions to the formatting of platform information. + - Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly. + - Overview display and hidden region visibility stored in Jalview projects + - Updated faq and documentation urls in splashscreen and help documentation ### Development and Deployment - + - Installers built with install4j10 - Create separate gradle test task for some tests - - Allow gradle build to create suffixed DEVELOP-... builds with channel appbase + - Prevent gradle test on macOS continuously grabbing focus -- Allow gradle build to create suffixed DEVELOP-... builds with channel appbase ++- Allow gradle build to create suffixed DEVELOP-... builds with channel + - Update .jvl generation in build.gradle for jalview branch builds - Jalview bio.tools description maintained under jalview's git repo and bundled with source release + - Output stderr and stdout when running tests via gradle + - New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress) - ## Issues Resolved - Jmol view not always centred on structures when multiple structures are viewed - - Cancelling interactive calculation leaves empty progress bar. - Unsaved Alignment windows close without prompting to save, individually or at application quit. - Can quit Jalview while 'save project' is in progress - 'Use original colours' option of colour by annotation not honoured when restoring view from project diff --cc src/jalview/gui/AlignFrame.java index d82fa42,1aca4d4..7116cf3 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@@ -60,7 -61,9 +61,8 @@@ import java.util.List 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; @@@ -70,7 -73,7 +72,8 @@@ import javax.swing.JLayeredPane 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; diff --cc src/jalview/gui/CalculationChooser.java index 21d985c,4e22a74..80102cb --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@@ -88,9 -81,22 +90,24 @@@ public class CalculationChooser extend 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; @@@ -234,9 -227,13 +255,14 @@@ } }; 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! @@@ -545,11 -606,18 +636,20 @@@ 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); } diff --cc src/jalview/gui/PairwiseAlignPanel.java index 087d7f6,b5b6ffc..af7913b --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@@ -170,36 -104,19 +170,36 @@@ System.out.println("Creating pap") 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) {