From a0f8ff1f0e3b8cea1c3c2c03c774dfb8251ade77 Mon Sep 17 00:00:00 2001 From: BobHanson Date: Mon, 1 Jun 2020 17:25:24 -0500 Subject: [PATCH 1/1] JAL-3626 from JAL-3253-applet CalculationChooser -- dissociated from panel for static access by JavaScript --- src/jalview/gui/CalculationChooser.java | 165 +++++++++++++++++++++++++------ src/jalview/gui/Preferences.java | 2 + 2 files changed, 138 insertions(+), 29 deletions(-) diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 097a5a0..5248306 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -62,8 +62,13 @@ import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; /** - * A dialog where a user can choose and action Tree or PCA calculation options + * A dialog where a user can choose and action Tree or PCA calculation options. + * + * Allows also for dialog-free static methods openPCAPanel(...) and + * openTreePanel(...) for scripted use. + * */ +@SuppressWarnings("serial") public class CalculationChooser extends JPanel { /* @@ -74,7 +79,7 @@ public class CalculationChooser extends JPanel */ private static boolean treeMatchGaps = true; - private static final Font VERDANA_11PT = new Font("Verdana", 0, 11); + private static Font VERDANA_11PT; private static final int MIN_TREE_SELECTION = 3; @@ -102,7 +107,7 @@ public class CalculationChooser extends JPanel private JCheckBox shorterSequence; - final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer(); + private static ComboBoxTooltipRenderer renderer; // BH was not static List tips = new ArrayList<>(); @@ -112,6 +117,37 @@ public class CalculationChooser extends JPanel private PCAPanel pcaPanel; /** + * Open a new Tree panel on the desktop statically. Params are standard (not + * set by Groovy). No dialog is opened. + * + * @param af + * @param treeType + * @param modelName + * @return null if successful; the string + * "label.you_need_at_least_n_sequences" if number of sequences + * selected is inappropriate + */ + public static Object openTreePanel(AlignFrame af, String treeType, + String modelName) + { + return openTreePanel(af, treeType, modelName, null); + } + + /** + * public static method for JalviewJS API to open a PCAPanel without + * necessarily using a dialog. + * + * @param af + * @param modelName + * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences" + * if number of sequences selected is inappropriate + */ + public static Object openPcaPanel(AlignFrame af, String modelName) + { + return openPcaPanel(af, modelName, null); + } + + /** * Constructor * * @param af @@ -232,6 +268,10 @@ public class CalculationChooser extends JPanel paramsPanel.add(includeGappedColumns); paramsPanel.add(shorterSequence); + if (VERDANA_11PT == null) + { + VERDANA_11PT = new Font("Verdana", 0, 11); + } /* * OK / Cancel buttons */ @@ -380,7 +420,11 @@ public class CalculationChooser extends JPanel */ protected JComboBox buildModelOptionsList() { - final JComboBox scoreModelsCombo = new JComboBox<>(); + JComboBox scoreModelsCombo = new JComboBox<>(); + if (renderer == null) + { + renderer = new ComboBoxTooltipRenderer(); + } scoreModelsCombo.setRenderer(renderer); /* @@ -500,7 +544,8 @@ public class CalculationChooser extends JPanel * for backwards compatibility with Jalview < 2.8 (JAL-2962) */ if (nucleotide && forPca - && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false)) + && Cache.getDefault(Preferences.BLOSUM62_PCA_FOR_NUCLEOTIDE, + false)) { filtered.add(scoreModels.getBlosum62()); } @@ -537,6 +582,63 @@ public class CalculationChooser extends JPanel */ protected void openTreePanel(String modelName, SimilarityParamsI params) { + Object ret = openTreePanel(af, + neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING + : TreeBuilder.AVERAGE_DISTANCE, + modelName, params); + if (ret instanceof String) + { + JvOptionPane.showMessageDialog(this, // was opening on Desktop? + MessageManager.formatMessage( + (String) ret, + MIN_TREE_SELECTION), + MessageManager.getString("label.not_enough_sequences"), + JvOptionPane.WARNING_MESSAGE); + + } + } + + /** + * Open a new PCA panel on the desktop + * + * @param modelName + * @param params + */ + protected void openPcaPanel(String modelName, SimilarityParamsI params) + { + Object ret = openPcaPanel(af, modelName, params); + if (ret instanceof String) + { + JvOptionPane.showInternalMessageDialog(this, + MessageManager.formatMessage( + (String) ret, + MIN_PCA_SELECTION), + MessageManager + .getString("label.sequence_selection_insufficient"), + JvOptionPane.WARNING_MESSAGE); + } + else + { + // only used for test suite + pcaPanel = (PCAPanel) ret; + } + + } + + /** + * Open a new Tree panel on the desktop statically + * + * @param af + * @param treeType + * @param modelName + * @param params + * @return null, or the string "label.you_need_at_least_n_sequences" if number + * of sequences selected is inappropriate + */ + public static Object openTreePanel(AlignFrame af, String treeType, + String modelName, SimilarityParamsI params) + { + /* * gui validation shouldn't allow insufficient sequences here, but leave * this check in in case this method gets exposed programmatically in future @@ -545,56 +647,58 @@ public class CalculationChooser extends JPanel SequenceGroup sg = viewport.getSelectionGroup(); if (sg != null && sg.getSize() < MIN_TREE_SELECTION) { - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.you_need_at_least_n_sequences", - MIN_TREE_SELECTION), - MessageManager.getString("label.not_enough_sequences"), - JvOptionPane.WARNING_MESSAGE); - return; + return "label.you_need_at_least_n_sequences"; + } + + if (params == null) + { + params = getSimilarityParameters(false); } - String treeType = neighbourJoining.isSelected() - ? TreeBuilder.NEIGHBOUR_JOINING - : TreeBuilder.AVERAGE_DISTANCE; af.newTreePanel(treeType, modelName, params); + return null; } /** - * Open a new PCA panel on the desktop + * public static method for JalviewJS API * + * @param af * @param modelName * @param params + * @return the PCAPanel, or null if number of sequences selected is + * inappropriate */ - protected void openPcaPanel(String modelName, SimilarityParamsI params) + public static Object openPcaPanel(AlignFrame af, String modelName, + SimilarityParamsI params) { + AlignViewport viewport = af.getViewport(); /* * gui validation shouldn't allow insufficient sequences here, but leave * this check in in case this method gets exposed programmatically in future + * + * */ if (((viewport.getSelectionGroup() != null) && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) && (viewport.getSelectionGroup().getSize() > 0)) || (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION)) { - JvOptionPane.showInternalMessageDialog(this, - MessageManager.formatMessage( - "label.you_need_at_least_n_sequences", - MIN_PCA_SELECTION), - MessageManager - .getString("label.sequence_selection_insufficient"), - JvOptionPane.WARNING_MESSAGE); - return; + return "label.you_need_at_least_n_sequences"; + } + + if (params == null) + { + params = getSimilarityParameters(true); } /* * construct the panel and kick off its calculation thread */ - pcaPanel = new PCAPanel(af.alignPanel, modelName, params); - new Thread(pcaPanel).start(); - + PCAPanel pcap = new PCAPanel(af.alignPanel, modelName, params); + new Thread(pcap).start(); + return pcap; } /** @@ -610,6 +714,7 @@ public class CalculationChooser extends JPanel } } + /** * Returns a data bean holding parameters for similarity (or distance) model * calculation @@ -617,7 +722,8 @@ public class CalculationChooser extends JPanel * @param doPCA * @return */ - protected SimilarityParamsI getSimilarityParameters(boolean doPCA) + public static SimilarityParamsI getSimilarityParameters( + boolean doPCA) { // commented out: parameter choices read from gui widgets // SimilarityParamsI params = new SimilarityParams( @@ -638,6 +744,7 @@ public class CalculationChooser extends JPanel return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength); + } /** diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 66962d6..bd795af 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -100,6 +100,8 @@ public class Preferences extends GPreferences public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS"; + public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE"; + public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS"; public static final String CHIMERA_PATH = "CHIMERA_PATH"; -- 1.7.10.2