X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=6d8457412b414866ca8646372e3b40e925993309;hb=efee78d45ceeb879d98fedd399a71d84a5ecd5f8;hp=2e9731d42c43e3beb79531f1078cdc1a6deb480f;hpb=dc78f37f49146f6339815e93598159d0c1ddc4c7;p=jalview.git diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 2e9731d..6d84574 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -45,6 +45,7 @@ import java.io.FileOutputStream; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; +import java.io.Reader; import java.util.Arrays; import java.util.Comparator; import java.util.HashMap; @@ -103,6 +104,8 @@ import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; import jalview.gui.Help.HelpId; import jalview.gui.JalviewColourChooser.ColourChooserListener; +import jalview.io.DataSourceType; +import jalview.io.FileParse; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.schemes.FeatureColour; @@ -955,6 +958,65 @@ public class FeatureSettings extends JPanel chooser.showOpenDialog(this); } + public static boolean loadFeatureSettingsFile(FeatureRenderer fr, + File file) throws Exception + { + InputStreamReader in = new InputStreamReader(new FileInputStream(file), + "UTF-8"); + return loadFeatureSettingsFile(fr, in); + } + + public static void loadFeatureSettingsFile( + FeatureRenderer featureRenderer, Object fileObject, + DataSourceType sourceType) throws Exception + { + FileParse fp = new FileParse(fileObject, sourceType); + loadFeatureSettingsFile(featureRenderer, fp.getReader()); + } + + private static boolean loadFeatureSettingsFile(FeatureRenderer fr, + Reader in) throws Exception + { + JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.jalview"); + javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); + XMLStreamReader streamReader = XMLInputFactory.newInstance() + .createXMLStreamReader(in); + JAXBElement jbe = um.unmarshal(streamReader, + JalviewUserColours.class); + JalviewUserColours jucs = jbe.getValue(); + + // JalviewUserColours jucs = JalviewUserColours.unmarshal(in); + + /* + * load feature colours + */ + for (int i = jucs.getColour().size() - 1; i >= 0; i--) + { + Colour newcol = jucs.getColour().get(i); + FeatureColourI colour = jalview.project.Jalview2XML + .parseColour(newcol); + fr.setColour(newcol.getName(), colour); + fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size()); + } + + /* + * load feature filters; loaded filters will replace any that are + * currently defined, other defined filters are left unchanged + */ + for (int i = 0; i < jucs.getFilter().size(); i++) + { + Filter filterModel = jucs.getFilter().get(i); + String featureType = filterModel.getFeatureType(); + FeatureMatcherSetI filter = jalview.project.Jalview2XML + .parseFilter(featureType, filterModel.getMatcherSet()); + if (!filter.isEmpty()) + { + fr.setFeatureFilter(featureType, filter); + } + } + return true; + } + /** * Loads feature colours and filters from XML stored in the given file * @@ -962,50 +1024,21 @@ public class FeatureSettings extends JPanel */ void load(File file) { + load(file, DataSourceType.FILE); + } + + /** + * Loads feature colours and filters from XML at a specified source + * + * @param file + * - string or file or other object that allows FileParse to be + * created + */ + void load(Object file, DataSourceType sourceType) + { try { - InputStreamReader in = new InputStreamReader( - new FileInputStream(file), "UTF-8"); - - JAXBContext jc = JAXBContext - .newInstance("jalview.xml.binding.jalview"); - javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); - XMLStreamReader streamReader = XMLInputFactory.newInstance() - .createXMLStreamReader(in); - JAXBElement jbe = um.unmarshal(streamReader, - JalviewUserColours.class); - JalviewUserColours jucs = jbe.getValue(); - - // JalviewUserColours jucs = JalviewUserColours.unmarshal(in); - - /* - * load feature colours - */ - for (int i = jucs.getColour().size() - 1; i >= 0; i--) - { - Colour newcol = jucs.getColour().get(i); - FeatureColourI colour = jalview.project.Jalview2XML - .parseColour(newcol); - fr.setColour(newcol.getName(), colour); - fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size()); - } - - /* - * load feature filters; loaded filters will replace any that are - * currently defined, other defined filters are left unchanged - */ - for (int i = 0; i < jucs.getFilter().size(); i++) - { - Filter filterModel = jucs.getFilter().get(i); - String featureType = filterModel.getFeatureType(); - FeatureMatcherSetI filter = jalview.project.Jalview2XML - .parseFilter(featureType, filterModel.getMatcherSet()); - if (!filter.isEmpty()) - { - fr.setFeatureFilter(featureType, filter); - } - } - + loadFeatureSettingsFile(fr, file, sourceType); /* * update feature settings table */ @@ -1019,7 +1052,8 @@ public class FeatureSettings extends JPanel } } catch (Exception ex) { - System.out.println("Error loading User Colour File\n" + ex); + jalview.bin.Console + .outPrintln("Error loading User Colour File\n" + ex); } } @@ -1608,7 +1642,7 @@ public class FeatureSettings extends JPanel { Color newColor = gcol.getMaxColour(); comp.setBackground(newColor); - // System.err.println("Width is " + w / 2); + // jalview.bin.Console.errPrintln("Width is " + w / 2); Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr); comp.setIcon(ficon); // tt+="RGB value: Max (" + newColor.getRed() + ", " @@ -1787,11 +1821,15 @@ public class FeatureSettings extends JPanel { FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter; setOpaque(true); - String asText = theFilter.toString(); setBackground(tbl.getBackground()); - this.setText(asText); this.setIcon(null); + if (theFilter != null) + { + String asText = theFilter.toString(); + this.setText(asText); + } + if (isSelected) { if (selectedBorder == null) @@ -1881,6 +1919,9 @@ public class FeatureSettings extends JPanel */ String ttl = MessageManager .formatMessage("label.select_colour_for", type); + Object last = (Boolean) table.getValueAt(selectedRow, + SHOW_COLUMN); + table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); ColourChooserListener listener = new ColourChooserListener() { @Override @@ -1888,12 +1929,14 @@ public class FeatureSettings extends JPanel { currentColor = new FeatureColour(c); table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN); + table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); fireEditingStopped(); } @Override public void cancel() { + table.setValueAt(last, selectedRow, SHOW_COLUMN); fireEditingStopped(); } }; @@ -1905,7 +1948,10 @@ public class FeatureSettings extends JPanel /* * variable colour and filters dialog */ - chooser = new FeatureTypeSettings(fr, type); + boolean last = (Boolean) table.getValueAt(selectedRow, + SHOW_COLUMN); + table.setValueAt(Boolean.TRUE, selectedRow, SHOW_COLUMN); + chooser = new FeatureTypeSettings(fr, type, last); if (!Platform.isJS()) /** * Java only @@ -2031,7 +2077,11 @@ public class FeatureSettings extends JPanel { if (button == e.getSource()) { - FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type); + boolean last = fr.getFeaturesDisplayed().isVisible(type); + ((FeatureTableModel) table.getModel()).setValueAt(Boolean.TRUE, + rowSelected, SHOW_COLUMN); + FeatureTypeSettings chooser = new FeatureTypeSettings(fr, type, + last); chooser.addActionListener(this); chooser.setRequestFocusEnabled(true); chooser.requestFocus(); @@ -2063,6 +2113,8 @@ public class FeatureSettings extends JPanel .getData()[rowSelected]; data[COLOUR_COLUMN] = currentColor; data[FILTER_COLUMN] = currentFilter; + data[SHOW_COLUMN] = fr.getFeaturesDisplayed().isVisible(type); + fireEditingStopped(); // SwingJS needs an explicit repaint() here, // rather than relying upon no validation having