import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
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
{
/*
*/
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;
private JCheckBox shorterSequence;
- final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
+ private static ComboBoxTooltipRenderer renderer; // BH was not static
- List<String> tips = new ArrayList<String>();
+ List<String> tips = new ArrayList<>();
/*
* the most recently opened PCA results panel
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
pca = new JRadioButton(
MessageManager.getString("label.principal_component_analysis"));
pca.setOpaque(false);
+
neighbourJoining = new JRadioButton(
MessageManager.getString("label.tree_calc_nj"));
neighbourJoining.setSelected(true);
+ neighbourJoining.setOpaque(false);
+
averageDistance = new JRadioButton(
MessageManager.getString("label.tree_calc_av"));
- neighbourJoining.setOpaque(false);
+ averageDistance.setOpaque(false);
JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
calcChoicePanel.setOpaque(false);
JPanel treePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
treePanel.setOpaque(false);
- JvSwingUtils.createItalicTitledBorder(treePanel,
+ JvSwingUtils.createTitledBorder(treePanel,
MessageManager.getString("label.tree"), true);
// then copy the inset dimensions for the border-less PCA panel
paramsPanel.add(includeGappedColumns);
paramsPanel.add(shorterSequence);
+ if (VERDANA_11PT == null)
+ {
+ VERDANA_11PT = new Font("Verdana", 0, 11);
+ }
/*
* OK / Cancel buttons
*/
setMinimumSize(new Dimension(325, height - 10));
String title = MessageManager.getString("label.choose_calculation");
- if (af.getViewport().viewName != null)
+ if (af.getViewport().getViewName() != null)
{
- title = title + " (" + af.getViewport().viewName + ")";
+ title = title + " (" + af.getViewport().getViewName() + ")";
}
Desktop.addInternalFrame(frame, title, width, height, false);
};
});
+ validateCalcTypes();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+ JComboBox<String> scoreModelsCombo = new JComboBox<>();
+ if (renderer == null)
+ {
+ renderer = new ComboBoxTooltipRenderer();
+ }
scoreModelsCombo.setRenderer(renderer);
/*
{
Object curSel = comboBox.getSelectedItem();
toolTips.clear();
- DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+ DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
+
+ /*
+ * select the score models applicable to the alignment type
+ */
+ boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+ List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
+ pca.isSelected());
/*
* now we can actually add entries to the combobox,
* remembering their descriptions for tooltips
*/
- ScoreModels scoreModels = ScoreModels.getInstance();
boolean selectedIsPresent = false;
- for (ScoreModelI sm : scoreModels.getModels())
+ for (ScoreModelI sm : models)
{
- boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
- if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
+ if (curSel != null && sm.getName().equals(curSel))
{
- if (curSel != null && sm.getName().equals(curSel))
- {
- selectedIsPresent = true;
- curSel = sm.getName();
- }
- model.addElement(sm.getName());
-
- /*
- * tooltip is description if provided, else text lookup with
- * fallback on the model name
- */
- String tooltip = sm.getDescription();
- if (tooltip == null)
- {
- tooltip = MessageManager.getStringOrReturn("label.score_model_",
- sm.getName());
- }
- toolTips.add(tooltip);
+ selectedIsPresent = true;
+ curSel = sm.getName();
}
+ model.addElement(sm.getName());
+
+ /*
+ * tooltip is description if provided, else text lookup with
+ * fallback on the model name
+ */
+ String tooltip = sm.getDescription();
+ if (tooltip == null)
+ {
+ tooltip = MessageManager.getStringOrReturn("label.score_model_",
+ sm.getName());
+ }
+ toolTips.add(tooltip);
}
+
if (selectedIsPresent)
{
model.setSelectedItem(curSel);
}
/**
+ * Builds a list of score models which are applicable for the alignment and
+ * calculation type (peptide or generic models for protein, nucleotide or
+ * generic models for nucleotide).
+ * <p>
+ * As a special case, includes BLOSUM62 as an extra option for nucleotide PCA.
+ * This is for backwards compatibility with Jalview prior to 2.8 when BLOSUM62
+ * was the only score matrix supported. This is included if property
+ * BLOSUM62_PCA_FOR_NUCLEOTIDE is set to true in the Jalview properties file.
+ *
+ * @param nucleotide
+ * @param forPca
+ * @return
+ */
+ protected static List<ScoreModelI> getApplicableScoreModels(
+ boolean nucleotide, boolean forPca)
+ {
+ List<ScoreModelI> filtered = new ArrayList<>();
+
+ ScoreModels scoreModels = ScoreModels.getInstance();
+ for (ScoreModelI sm : scoreModels.getModels())
+ {
+ if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA())
+ {
+ filtered.add(sm);
+ }
+ }
+
+ /*
+ * special case: add BLOSUM62 as last option for nucleotide PCA,
+ * for backwards compatibility with Jalview < 2.8 (JAL-2962)
+ */
+ if (nucleotide && forPca
+ && Cache.getDefault(Preferences.BLOSUM62_PCA_FOR_NUCLEOTIDE,
+ false))
+ {
+ filtered.add(scoreModels.getBlosum62());
+ }
+
+ return filtered;
+ }
+
+ /**
* Open and calculate the selected tree or PCA on 'OK'
*/
protected void calculate_actionPerformed()
*/
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
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);
}
- pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
+
+ /*
+ * construct the panel and kick off its calculation thread
+ */
+ PCAPanel pcap = new PCAPanel(af.alignPanel, modelName, params);
+ new Thread(pcap).start();
+ return pcap;
}
/**
}
}
+
/**
* Returns a data bean holding parameters for similarity (or distance) model
* calculation
* @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(
return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
matchOnShortestLength);
+
}
/**
public PCAPanel getPcaPanel()
{
+ // only called for FreeUpMemoryTest
return pcaPanel;
}
}
git://source.jalview.org / jalview.git / blobdiff