import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.hmmer.HMMBuildThread;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
+import java.util.Scanner;
import javax.help.HelpSetException;
import javax.swing.JColorChooser;
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 SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
* .properties file as '|' separated strings
*/
- groupURLLinks = new ArrayList<String>();
+ groupURLLinks = new ArrayList<>();
}
JInternalFrame frame;
frame.setMinimumSize(new Dimension(width, height));
/*
+ * Set HMMER tab defaults
+ */
+ trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ isHMMERInstalled
+ .setSelected(Cache.getDefault("HMMER_INSTALLED", false));
+ if (Cache.getDefault("USE_UNIPROT", false))
+ {
+ uniprot.setSelected(true);
+ }
+ else
+ {
+ alignment.setSelected(true);
+ }
+ numberOfSequencesToKeepField
+ .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ installationLocation.setEnabled(isHMMERInstalled.isSelected());
+ hmmerPath.setEnabled(isHMMERInstalled.isSelected());
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+ hmmerPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateHMMERPath();
+ }
+ });
+
+ /*
* 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
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(trimTermini.isSelected()));
+ Cache.applicationProperties.setProperty("USE_UNIPROT",
+ Boolean.toString(uniprot.isSelected()));
+ Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
+ numberOfSequencesToKeepField.getText());
+ Cache.applicationProperties.setProperty(HMMER_PATH,
+ hmmerPath.getText());
+ boolean hmmerInstalled = isHMMERInstalled.isSelected();
+ Cache.applicationProperties.setProperty("HMMER_INSTALLED",
+ Boolean.toString(hmmerInstalled));
+ boolean hmmerFunctioning = validateHMMERPath(false);
+ Cache.applicationProperties.setProperty("HMMER_FUNCTIONING",
+ Boolean.toString(hmmerFunctioning));
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false;
+ for (AlignFrame frame : frames)
+ {
+ frame.updateHMMERStatus(hmmerStatus);
+ }
+
+
+ trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ if (Cache.getDefault("USE_UNIPROT", false))
+ {
+ uniprot.setSelected(true);
+ }
+ else
+ {
+ alignment.setSelected(true);
+ }
+ numberOfSequencesToKeepField
+ .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+ /*
* Save Structure settings
*/
Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
structureTab.requestFocusInWindow();
return false;
}
+ if (isHMMERInstalled.isSelected())
+ {
+ if (!validateHMMER())
+ {
+ hmmerTab.requestFocusInWindow();
+ return false;
+ }
+ }
return true;
}
}
+ @Override
+ protected boolean validateHMMER()
+ {
+ return validateHMMERPath();
+
+ }
+
/**
* DOCUMENT ME!
*/
&& (identity.isSelected() || showGroupConsensus.isSelected()));
showConsensLogo.setEnabled(annotations.isSelected()
&& (identity.isSelected() || showGroupConsensus.isSelected()));
+ showInformationHistogram.setEnabled(annotations.isSelected());
+ showHMMLogo.setEnabled(annotations.isSelected());
}
@Override
}
return true;
}
+
+ /**
+ * Returns true if hmmer path contains the necessary valid executables, else
+ * show an error dialog (if showing dialog).
+ */
+ private boolean validateHMMERPath(boolean showDialog)
+ {
+ int missing = 0;
+ String message = "";
+ String folder = hmmerPath.getText().trim();
+ if (folder.length() > 0)
+ {
+ File f = new File(folder);
+ if (!f.exists())
+ {
+ if (showDialog)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.folder_not_exists"),
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return false;
+ }
+ AlignmentI alignment = new Alignment(
+ new SequenceI[]
+ { new Sequence("test", "WLWL", 0, 3) });
+ if (canExecute(folder + "/hmmbuild"))
+ {
+ validateHMMBuild(alignment);
+ }
+ else
+ {
+ message += MessageManager.getString("label.hmmbuild_not_found")
+ + "\n";
+ missing++;
+ }
+
+
+ if (canExecute(folder + "/hmmalign"))
+ {
+
+ }
+ else
+ {
+ message += MessageManager.getString("label.hmmalign_not_found")
+ + "\n";
+ missing++;
+ }
+
+
+ if (canExecute(folder + "/hmmsearch"))
+ {
+
+ }
+ else
+ {
+ message += MessageManager.getString("label.hmmsearch_not_found")
+ + "\n";
+ missing++;
+ }
+ }
+
+ if (missing > 0)
+ {
+ if (missing < 3)
+ {
+ if (showDialog)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return false;
+ }
+ else
+ {
+ if (showDialog)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.no_binaries"),
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Runs hmmbuild to check if it is working. While doing this it parses the
+ * version of HMMER.
+ *
+ * @param frame
+ * @return
+ */
+ public boolean validateHMMBuild(AlignmentI alignment)
+ {
+ HMMBuildThread hmmbuild = new HMMBuildThread(alignment);
+ hmmbuild.hmmbuildWaitTillComplete();
+ SequenceI hmmSeq = alignment.getSequenceAt(1);
+ HiddenMarkovModel hmm;
+ if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null)
+ {
+ hmm = hmmSeq.getHMM();
+
+ if (hmm.getNumberOfSymbols() < 1)
+ {
+ return false;
+ }
+ }
+ else
+ {
+ return false;
+ }
+
+ String header = hmm.getFileHeader();
+ if (header == null)
+ {
+ return false;
+ }
+ else
+ {
+ Scanner scanner = new Scanner(header);
+ scanner.next();
+ String string = scanner.next();
+ String version = string.substring(1);
+ Cache.setProperty("HMMER_VERSION", version);
+ scanner.close();
+
+ }
+ return true;
+ }
+
+
+ private boolean validateHMMERPath()
+ {
+ return validateHMMERPath(true);
+ }
/**
* If Chimera is selected, check it can be found on default or user-specified
git://source.jalview.org / jalview.git / blobdiff