X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=2c454a40105db7b5808c2e5dcd2f95c854157ecb;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=8ce3e626874c14b837dbd05bb9945fc8afcfff79;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 8ce3e62..2c454a4 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -20,21 +20,51 @@ */ package jalview.appletgui; -import java.util.*; -import java.util.List; -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.AlignmentSorter; -import jalview.commands.OrderCommand; -import jalview.datamodel.*; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; +import jalview.api.FeatureColourI; +import jalview.api.FeatureSettingsControllerI; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceFeature; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Checkbox; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Image; +import java.awt.Label; +import java.awt.MenuItem; +import java.awt.Panel; +import java.awt.PopupMenu; +import java.awt.ScrollPane; +import java.awt.Scrollbar; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.event.InputEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.util.Arrays; +import java.util.Enumeration; +import java.util.List; +import java.util.Map; +import java.util.Vector; + public class FeatureSettings extends Panel implements ItemListener, MouseListener, MouseMotionListener, ActionListener, - AdjustmentListener + AdjustmentListener, FeatureSettingsControllerI { FeatureRenderer fr; @@ -64,14 +94,7 @@ public class FeatureSettings extends Panel implements ItemListener, transparency = new Scrollbar(Scrollbar.HORIZONTAL, 100 - (int) (fr.getTransparency() * 100), 1, 1, 100); - if (fr.isTransparencyAvailable()) - { - transparency.addAdjustmentListener(this); - } - else - { - transparency.setEnabled(false); - } + transparency.addAdjustmentListener(this); java.net.URL url = getClass().getResource("/images/link.gif"); if (url != null) @@ -84,12 +107,13 @@ public class FeatureSettings extends Panel implements ItemListener, fr.findAllFeatures(true); // was default - now true to make all visible } - setTableData(); + discoverAllFeatureData(); this.setLayout(new BorderLayout()); scrollPane = new ScrollPane(); scrollPane.add(featurePanel); - if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0) + if (fr.getAllFeatureColours() != null + && fr.getAllFeatureColours().size() > 0) { add(scrollPane, BorderLayout.CENTER); } @@ -102,17 +126,8 @@ public class FeatureSettings extends Panel implements ItemListener, Panel tPanel = new Panel(new BorderLayout()); - if (fr.isTransparencyAvailable()) - { - tPanel.add(transparency, BorderLayout.CENTER); - tPanel.add(new Label("Transparency"), BorderLayout.EAST); - } - else - { - tPanel.add( - new Label("Transparency not available in this web browser"), - BorderLayout.CENTER); - } + tPanel.add(transparency, BorderLayout.CENTER); + tPanel.add(new Label("Transparency"), BorderLayout.EAST); lowerPanel.add(tPanel, BorderLayout.SOUTH); @@ -120,10 +135,11 @@ public class FeatureSettings extends Panel implements ItemListener, if (groupPanel != null) { - groupPanel - .setLayout(new GridLayout( - (fr.getFeatureGroupsSize()) / 4 + 1, - 4)); // JBPNote - this was scaled on number of visible groups. seems broken + groupPanel.setLayout(new GridLayout( + (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was + // scaled on number of + // visible groups. seems + // broken groupPanel.validate(); add(groupPanel, BorderLayout.NORTH); @@ -133,6 +149,7 @@ public class FeatureSettings extends Panel implements ItemListener, final FeatureSettings me = this; frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { if (me.av.featureSettings == me) @@ -149,10 +166,11 @@ public class FeatureSettings extends Panel implements ItemListener, height = Math.min(400, height); int width = 300; jalview.bin.JalviewLite.addFrame(frame, - MessageManager.getString("label.feature_settings"), width, - height); + MessageManager.getString("label.sequence_feature_settings"), + width, height); } + @Override public void paint(Graphics g) { g.setColor(Color.black); @@ -166,14 +184,13 @@ public class FeatureSettings extends Panel implements ItemListener, 60); } - protected void popupSort(final MyCheckbox check, final Hashtable minmax, - int x, int y) + protected void popupSort(final MyCheckbox check, + final Map minmax, int x, int y) { final String type = check.type; - final Object typeCol = fr.getFeatureStyle(type); - java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage( - "label.settings_for_type", new String[] - { type })); + final FeatureColourI typeCol = fr.getFeatureStyle(type); + PopupMenu men = new PopupMenu(MessageManager.formatMessage( + "label.settings_for_type", new String[] { type })); java.awt.MenuItem scr = new MenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); @@ -181,10 +198,11 @@ public class FeatureSettings extends Panel implements ItemListener, scr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[] - { type }); + me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays + .asList(new String[] { type })); } }); @@ -193,17 +211,19 @@ public class FeatureSettings extends Panel implements ItemListener, dens.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[] - { type }); + me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays + .asList(new String[] { type })); } }); men.add(dens); + if (minmax != null) { - final Object typeMinMax = minmax.get(type); + final float[][] typeMinMax = minmax.get(type); /* * final java.awt.CheckboxMenuItem chb = new * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the @@ -216,20 +236,21 @@ public class FeatureSettings extends Panel implements ItemListener, * * }); men.add(chb); */ - if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null) + if (typeMinMax != null && typeMinMax[0] != null) { // graduated colourschemes for those where minmax exists for the // positional features MenuItem mxcol = new MenuItem( - (typeCol instanceof Color) ? "Graduated Colour" + (typeCol.isSimpleColour()) ? "Graduated Colour" : "Single Colour"); men.add(mxcol); mxcol.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - if (typeCol instanceof Color) + if (typeCol.isSimpleColour()) { new FeatureColourChooser(me, type); // write back the current colour object to update the table @@ -237,21 +258,73 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - new UserDefinedColours(me, check.type, - ((GraduatedColor) typeCol)); + new UserDefinedColours(me, check.type, typeCol); } } }); } } + + MenuItem selectContaining = new MenuItem( + MessageManager.getString("label.select_columns_containing")); + selectContaining.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, + false, type); + } + }); + men.add(selectContaining); + + MenuItem selectNotContaining = new MenuItem( + MessageManager.getString("label.select_columns_not_containing")); + selectNotContaining.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, + false, type); + } + }); + men.add(selectNotContaining); + + MenuItem hideContaining = new MenuItem( + MessageManager.getString("label.hide_columns_containing")); + hideContaining.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideFeatureColumns(type, true); + } + }); + men.add(hideContaining); + + MenuItem hideNotContaining = new MenuItem( + MessageManager.getString("label.hide_columns_not_containing")); + hideNotContaining.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideFeatureColumns(type, false); + } + }); + men.add(hideNotContaining); + this.featurePanel.add(men); men.show(this.featurePanel, x, y); } - public void setTableData() + @Override + public void discoverAllFeatureData() { - if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0) + if (fr.getAllFeatureColours() != null + && fr.getAllFeatureColours().size() > 0) { rebuildGroups(); @@ -276,12 +349,10 @@ public class FeatureSettings extends Panel implements ItemListener, } // TODO: JAL-964 - smoothly incorporate new group entries if panel already // displayed and new groups present - for (String group:(List)fr.getFeatureGroups()) + for (String group : fr.getFeatureGroups()) { boolean vis = fr.checkGroupVisibility(group, false); - Checkbox check = new MyCheckbox(group, vis, - (fr.featureLinks != null && fr.featureLinks - .containsKey(group))); + Checkbox check = new MyCheckbox(group, vis, false); check.addMouseListener(this); check.setFont(new Font("Serif", Font.BOLD, 12)); check.addItemListener(groupItemListener); @@ -294,13 +365,14 @@ public class FeatureSettings extends Panel implements ItemListener, groupPanel.validate(); } } + // This routine adds and removes checkboxes depending on // Group selection states void resetTable(boolean groupsChanged) { SequenceFeature[] tmpfeatures; String group = null, type; - Vector visibleChecks = new Vector(); + Vector visibleChecks = new Vector(); AlignmentI alignment = av.getAlignment(); for (int i = 0; i < alignment.getHeight(); i++) { @@ -366,7 +438,7 @@ public class FeatureSettings extends Panel implements ItemListener, // now add checkboxes which should be visible, // if they have not already been added - Enumeration en = visibleChecks.elements(); + Enumeration en = visibleChecks.elements(); while (en.hasMoreElements()) { @@ -418,10 +490,7 @@ public class FeatureSettings extends Panel implements ItemListener, selected = true; } - check = new MyCheckbox( - type, - selected, - (fr.featureLinks != null && fr.featureLinks.containsKey(type)), + check = new MyCheckbox(type, selected, false, fr.getFeatureStyle(type)); check.addMouseListener(this); @@ -440,6 +509,7 @@ public class FeatureSettings extends Panel implements ItemListener, } } + @Override public void actionPerformed(ActionEvent evt) { for (int i = 0; i < featurePanel.getComponentCount(); i++) @@ -450,11 +520,13 @@ public class FeatureSettings extends Panel implements ItemListener, selectionChanged(); } - private ItemListener groupItemListener = new ItemListener() { - public void itemStateChanged(ItemEvent evt) { + private ItemListener groupItemListener = new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent evt) + { Checkbox source = (Checkbox) evt.getSource(); - fr.setGroupVisibility(source.getLabel(), - source.getState()); + fr.setGroupVisibility(source.getLabel(), source.getState()); ap.seqPanel.seqCanvas.repaint(); if (ap.overviewPanel != null) { @@ -464,6 +536,8 @@ public class FeatureSettings extends Panel implements ItemListener, return; }; }; + + @Override public void itemStateChanged(ItemEvent evt) { selectionChanged(); @@ -497,22 +571,7 @@ public class FeatureSettings extends Panel implements ItemListener, boolean dragging = false; - public void mousePressed(MouseEvent evt) - { - - selectedCheck = (MyCheckbox) evt.getSource(); - - if (fr.featureLinks != null - && fr.featureLinks.containsKey(selectedCheck.type)) - { - if (evt.getX() > selectedCheck.stringWidth + 20) - { - evt.consume(); - } - } - - } - + @Override public void mouseDragged(MouseEvent evt) { if (((Component) evt.getSource()).getParent() != featurePanel) @@ -522,6 +581,7 @@ public class FeatureSettings extends Panel implements ItemListener, dragging = true; } + @Override public void mouseReleased(MouseEvent evt) { if (((Component) evt.getSource()).getParent() != featurePanel) @@ -574,17 +634,9 @@ public class FeatureSettings extends Panel implements ItemListener, } } - public void setUserColour(String feature, Object originalColour) + public void setUserColour(String feature, FeatureColourI originalColour) { - if (originalColour instanceof Color - || originalColour instanceof GraduatedColor) - { - fr.setColour(feature, originalColour); - } - else - { - throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object")); - } + fr.setColour(feature, originalColour); refreshTable(); } @@ -595,14 +647,17 @@ public class FeatureSettings extends Panel implements ItemListener, ap.paintAlignment(true); } + @Override public void mouseEntered(MouseEvent evt) { } + @Override public void mouseExited(MouseEvent evt) { } + @Override public void mouseClicked(MouseEvent evt) { MyCheckbox check = (MyCheckbox) evt.getSource(); @@ -610,16 +665,6 @@ public class FeatureSettings extends Panel implements ItemListener, { this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY()); } - if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type)) - { - if (evt.getX() > check.stringWidth + 20) - { - evt.consume(); - String link = fr.featureLinks.get(check.type).toString(); - ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), - link.substring(0, link.indexOf("|"))); - } - } if (check.getParent() != featurePanel) { @@ -628,10 +673,10 @@ public class FeatureSettings extends Panel implements ItemListener, if (evt.getClickCount() > 1) { - Object fcol = fr.getFeatureStyle(check.type); - if (fcol instanceof Color) + FeatureColourI fcol = fr.getFeatureStyle(check.type); + if (fcol.isSimpleColour()) { - new UserDefinedColours(this, check.type, (Color) fcol); + new UserDefinedColours(this, check.type, fcol.getColour()); } else { @@ -642,13 +687,15 @@ public class FeatureSettings extends Panel implements ItemListener, } } + @Override public void mouseMoved(MouseEvent evt) { } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { - fr.setTransparency((float) (100 - transparency.getValue()) / 100f); + fr.setTransparency((100 - transparency.getValue()) / 100f); ap.seqPanel.seqCanvas.repaint(); } @@ -661,47 +708,34 @@ public class FeatureSettings extends Panel implements ItemListener, boolean hasLink; - GraduatedColor gcol; - - Color col; + FeatureColourI col; - public void updateColor(Object newcol) + public void updateColor(FeatureColourI newcol) { - if (newcol instanceof Color) + col = newcol; + if (col.isSimpleColour()) { - col = (Color) newcol; - gcol = null; - } - else if (newcol instanceof GraduatedColor) - { - gcol = (GraduatedColor) newcol; - col = null; - } - else - { - throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox")); - } - if (col != null) - { - setBackground(col); + setBackground(col.getColour()); } else { String vlabel = type; - if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + if (col.isAboveThreshold()) { - vlabel += " " - + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" - : "(<)"); + vlabel += " (>)"; } - if (gcol.isColourByLabel()) + else if (col.isBelowThreshold()) + { + vlabel += " (<)"; + } + if (col.isColourByLabel()) { setBackground(Color.white); vlabel += " (by Label)"; } else { - setBackground(gcol.getMinColor()); + setBackground(col.getMinColour()); } this.setLabel(vlabel); } @@ -718,18 +752,19 @@ public class FeatureSettings extends Panel implements ItemListener, } public MyCheckbox(String type, boolean selected, boolean b, - Object featureStyle) + FeatureColourI featureStyle) { this(type, selected, b); updateColor(featureStyle); } + @Override public void paint(Graphics g) { Dimension d = getSize(); - if (gcol != null) + if (col != null) { - if (gcol.isColourByLabel()) + if (col.isColourByLabel()) { g.setColor(Color.white); g.fillRect(d.width / 2, 0, d.width / 2, d.height); @@ -745,9 +780,9 @@ public class FeatureSettings extends Panel implements ItemListener, */ } - else + else if (col.isGraduatedColour()) { - Color maxCol = gcol.getMaxColor(); + Color maxCol = col.getMaxColour(); g.setColor(maxCol); g.fillRect(d.width / 2, 0, d.width / 2, d.height); @@ -762,4 +797,30 @@ public class FeatureSettings extends Panel implements ItemListener, } } + /** + * Hide columns containing (or not containing) a given feature type + * + * @param type + * @param columnsContaining + */ + void hideFeatureColumns(final String type, boolean columnsContaining) + { + if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining, + false, false, type)) + { + if (ap.alignFrame.avc.markColumnsContainingFeatures( + !columnsContaining, false, false, type)) + { + ap.alignFrame.viewport.hideSelectedColumns(); + } + } + } + + @Override + public void mousePressed(MouseEvent e) + { + // TODO Auto-generated method stub + + } + }