import jalview.bin.Cache;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.hmmer.HmmerCommand;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.MouseEvent;
import java.io.File;
import java.util.ArrayList;
public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String HMMER_PATH = "HMMER_PATH";
+
+ public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
+
+ public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+ public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+
+ public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
+
+ public static final String GAP_COLOUR = "GAP_COLOUR";
+
+ public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
private static final int MIN_FONT_SIZE = 1;
private static final int MAX_FONT_SIZE = 30;
* .properties file as '|' separated strings
*/
- groupURLLinks = new ArrayList<String>();
+ groupURLLinks = new ArrayList<>();
}
JInternalFrame frame;
frame.setMinimumSize(new Dimension(width, height));
/*
+ * Set HMMER tab defaults
+ */
+ hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ if (Cache.getDefault("USE_UNIPROT", false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+ hmmerPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateHMMERPath(true);
+ }
+ });
+ hmmerPath.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ validateHMMERPath(true);
+ }
+ });
+
+ /*
* Set Visual tab defaults
*/
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
showConsensLogo
.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showInformationHistogram.setSelected(
+ Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
+ showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
showNpTooltip
.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
showDbRefTooltip
Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
/*
+ * Set overview panel defaults
+ */
+ gapColour.setBackground(
+ Cache.getDefaultColour(GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+ hiddenColour.setBackground(
+ Cache.getDefaultColour(HIDDEN_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+ useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
+ gapLabel.setEnabled(!useLegacyGap.isSelected());
+ gapColour.setEnabled(!useLegacyGap.isSelected());
+ showHiddenAtStart
+ .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
+
+ /*
* Set Structure tab defaults.
*/
final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
userIdWidth.setText(wi == null ? "" : wi.toString());
+ // TODO: refactor to use common enum via FormatAdapter and allow extension
+ // for new flat file formats
blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
Boolean.toString(showConsensHistogram.isSelected()));
Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
Boolean.toString(showConsensLogo.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
+ Boolean.toString(showConsensHistogram.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
+ Boolean.toString(showHMMLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
maxColour.getBackground());
/*
+ * Save HMMER settings
+ */
+ Cache.applicationProperties.setProperty("TRIM_TERMINI",
+ Boolean.toString(hmmrTrimTermini.isSelected()));
+ Cache.applicationProperties.setProperty("USE_UNIPROT",
+ Boolean.toString(hmmerBackgroundUniprot.isSelected()));
+ Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
+ hmmerSequenceCount.getText());
+ Cache.applicationProperties.setProperty(HMMER_PATH,
+ hmmerPath.getText());
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames != null && frames.length > 0)
+ {
+ for (AlignFrame f : frames)
+ {
+ f.updateHMMERStatus();
+ }
+ }
+
+ hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ if (Cache.getDefault("USE_UNIPROT", false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+ /*
+ * Save Overview settings
+ */
+ Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+ Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+ Boolean.toString(useLegacyGap.isSelected()));
+ Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+ Boolean.toString(showHiddenAtStart.isSelected()));
+
+ /*
* Save Structure settings
*/
Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
&& (identity.isSelected() || showGroupConsensus.isSelected()));
showConsensLogo.setEnabled(annotations.isSelected()
&& (identity.isSelected() || showGroupConsensus.isSelected()));
+ showInformationHistogram.setEnabled(annotations.isSelected());
+ showHMMLogo.setEnabled(annotations.isSelected());
}
@Override
}
@Override
+ public void gapColour_actionPerformed(JPanel gap)
+ {
+ if (!useLegacyGap.isSelected())
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_gap_colour"),
+ gapColour.getBackground());
+ if (col != null)
+ {
+ gap.setBackground(col);
+ }
+ gap.repaint();
+ }
+ }
+
+ @Override
+ public void hiddenColour_actionPerformed(JPanel hidden)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_hidden_colour"),
+ hiddenColour.getBackground());
+ if (col != null)
+ {
+ hidden.setBackground(col);
+ }
+ hidden.repaint();
+ }
+
+ @Override
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ boolean enabled = useLegacyGap.isSelected();
+ if (enabled)
+ {
+ gapColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
+ }
+ else
+ {
+ gapColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+ }
+ gapColour.setEnabled(!enabled);
+ gapLabel.setEnabled(!enabled);
+ }
+
+ @Override
+ protected void resetOvDefaults_actionPerformed(ActionEvent e)
+ {
+ useLegacyGap.setSelected(false);
+ useLegacyGaps_actionPerformed(null);
+ showHiddenAtStart.setSelected(true);
+ hiddenColour.setBackground(
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+ }
+
+ @Override
protected void userIdWidth_actionPerformed()
{
try
}
return true;
}
+
+ /**
+ * Returns true if hmmer path is to a folder that contains an executable
+ * hmmbuild or hmmbuild.exe, else false (optionally after showing a warning
+ * dialog)
+ */
+ @Override
+ protected boolean validateHMMERPath(boolean showWarning)
+ {
+ String folder = hmmerPath.getText().trim();
+
+ if (HmmerCommand.getExecutable(HmmerCommand.HMMBUILD, folder) != null)
+ {
+ return true;
+ }
+ if (showWarning && folder.length() > 0)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.hmmbuild_not_found"),
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return false;
+ }
+
+ /**
+ * Checks if a file can be executed
+ *
+ * @param path
+ * the path to the file
+ * @return
+ */
+ public boolean canExecute(String path)
+ {
+ File file = new File(path);
+ if (!file.canExecute())
+ {
+ file = new File(path + ".exe");
+ {
+ if (!file.canExecute())
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
/**
* If Chimera is selected, check it can be found on default or user-specified
git://source.jalview.org / jalview.git / blobdiff