--- /dev/null
+HMMER3/f [3.1b2 | February 2015]
+NAME uniref50
+LENG 148
+ALPH amino
+ RF no
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Mon Jun 12 14:32:05 2017
+NSEQ 15
+EFFN 0.648193
+CKSUM 2563184735
+STATS LOCAL MSV -10.0682 0.70956
+STATS LOCAL VITERBI -10.7870 0.70956
+STATS LOCAL FORWARD -4.6837 0.70956
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
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+ 0.10433 3.97705 2.52157 0.61958 0.77255 0.00000 *
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+ 0.08120 2.55114 * 0.46726 0.98542 0.00000 *
+//
action.show_html_source = Show HTML Source
action.print = Print...
action.web_service = Web Service
+action.hmmer = HMMER
action.cancel_job = Cancel Job
action.start_job = Start Job
action.revert = Revert
status.searching_for_pdb_structures = Searching for PDB Structures
status.opening_file_for = opening file for
status.colouring_chimera = Colouring Chimera
+status.running_hmmbuild = "Building hidden Markov model"
+status.running_hmmalign = "Creating alignment with hidden Markov model"
+status.running_hmmsearch = "Searching for matching sequences"
label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
label.font_too_small = Font size is too small
label.error_loading_file_params = Error loading file {0}
label.show_experimental = Enable experimental features
label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
label.warning_hidden = Warning: {0} {1} is currently hidden
+label.hmmalign = hmmalign
+label.hmmbuild = hmmbuild
+label.hmmbuild_group = Build HMM from Selected Group
+label.group_hmmbuild = Build HMM from Group
+label.hmmsearch = hmmsearch
+label.change_hmmer_location = HMMER Binaries Installation Location
+warn.null_hmm = Please ensure the alignment contains a hidden Markov model.
+label.ignore_below_background_frequency = Ignore Below Background Frequency
+label.information_description = Information content, measured in bits
+label.enter_location = Please enter the path of your HMMER binaries folder.
+label.invalid_hmmer_folder = The folder that you selected does not contain the necessary HMMER binaries.
+warn.no_selected_hmm = Please select a hidden Markov model sequence.
+label.select_hmm = Select HMM
+warn.no_sequence_data = No sequence data found.
+label.hmmer = HMMER
+label.trim_termini = Trim Non-Matching Termini
+label.no_of_sequences = Sequences Returned
+label.freq_alignment = Use Alignment Background Frequencies
+label.freq_uniprot = Use Uniprot Background Frequencies
+label.hmmalign_label = hmmalign Options
+label.hmmsearch_label = hmmsearch Options
+label.hmmbuild_not_found = The hmmbuild binary was not found.
+label.hmmalign_not_found = The hmmalign binary was not found.
+label.hmmsearch_not_found = The hmmsearch binary was not found.
+warn.hmmbuild_failed = hmmbuild was not found.
+warn.align_failed = hmmalign was not found.
+label.invalid_folder = Invalid Folder
+label.folder_not_exists = HMMER binaries not found. \n Please enter the path to the HMMER binaries (if installed).
+label.hmmer_installed = HMMER installed
\ No newline at end of file
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.Profile;
import jalview.datamodel.ProfileI;
import jalview.datamodel.Profiles;
import jalview.datamodel.ResidueCount.SymbolCounts;
import jalview.datamodel.SequenceI;
import jalview.ext.android.SparseIntArray;
+import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
import jalview.util.Format;
import jalview.util.MappingUtils;
{
public static final String PROFILE = "P";
+ private static final String AMINO = "amino";
+
+ private static final String DNA = "DNA";
+
+ private static final String RNA = "RNA";
+
/*
* Quick look-up of String value of char 'A' to 'Z'
*/
}
}
+
+
/**
* Calculate the consensus symbol(s) for each column in the given range.
*
}
/**
+ * Returns the full set of profiles for a hidden Markov model. The underlying
+ * data is the raw probabilities of a residue being emitted at each node,
+ * however the profiles returned by this function contain the percentage
+ * chance of a residue emission.
+ *
+ * @param hmm
+ * @param width
+ * The width of the Profile array (Profiles) to be returned.
+ * @param start
+ * The alignment column on which the first profile is based.
+ * @param end
+ * The alignment column on which the last profile is based.
+ * @param saveFullProfile
+ * Flag for saving the counts for each profile
+ * @param removeBelowBackground
+ * Flag for removing any characters with a match emission probability
+ * less than its background frequency
+ * @return
+ */
+ public static ProfilesI calculateHMMProfiles(final HiddenMarkovModel hmm,
+ int width, int start, int end, boolean saveFullProfile,
+ boolean removeBelowBackground)
+ {
+ ProfileI[] result = new ProfileI[width];
+ int symbolCount = hmm.getNumberOfSymbols();
+ for (int column = start; column < end; column++)
+ {
+ ResidueCount counts = new ResidueCount();
+ for (char symbol : hmm.getSymbols())
+ {
+ int value = getAnalogueCount(hmm, column, symbol,
+ removeBelowBackground);
+ counts.put(symbol, value);
+ }
+ int maxCount = counts.getModalCount();
+ String maxResidue = counts.getResiduesForCount(maxCount);
+ int gapCount = counts.getGapCount();
+ ProfileI profile = new Profile(symbolCount, gapCount, maxCount,
+ maxResidue);
+
+ if (saveFullProfile)
+ {
+ profile.setCounts(counts);
+ }
+
+ result[column] = profile;
+ }
+ return new Profiles(result);
+ }
+
+ /**
* Make an estimate of the profile size we are going to compute i.e. how many
* different characters may be present in it. Overestimating has a cost of
* using more memory than necessary. Underestimating has a cost of needing to
}
/**
+ * Derive the information annotations to be added to the alignment for
+ * display. This does not recompute the raw data, but may be called on a
+ * change in display options, such as 'ignore below background frequency',
+ * which may in turn result in a change in the derived values.
+ *
+ * @param information
+ * the annotation row to add annotations to
+ * @param profiles
+ * the source information data
+ * @param startCol
+ * start column (inclusive)
+ * @param endCol
+ * end column (exclusive)
+ * @param ignoreGaps
+ * if true, normalise residue percentages
+ * @param showSequenceLogo
+ * if true include all information symbols, else just show modal
+ * residue
+ * @param nseq
+ * number of sequences
+ */
+ public static void completeInformation(AlignmentAnnotation information,
+ ProfilesI profiles, int startCol, int endCol,
+ boolean ignoreBelowBackground,
+ boolean showSequenceLogo, long nseq)
+ {
+ // long now = System.currentTimeMillis();
+ if (information == null || information.annotations == null
+ || information.annotations.length < endCol)
+ {
+ /*
+ * called with a bad alignment annotation row
+ * wait for it to be initialised properly
+ */
+ return;
+ }
+
+ Float max = 0f;
+
+ for (int i = startCol; i < endCol; i++)
+ {
+ ProfileI profile = profiles.get(i);
+ if (profile == null)
+ {
+ /*
+ * happens if sequences calculated over were
+ * shorter than alignment width
+ */
+ information.annotations[i] = null;
+ return;
+ }
+
+ HiddenMarkovModel hmm;
+
+ SequenceI hmmSeq = information.sequenceRef;
+
+ hmm = hmmSeq.getHMM();
+
+ Float value = getInformationContent(i, hmm);
+
+ if (value > max)
+ {
+ max = value;
+ }
+
+ String description = value + " bits";
+ information.annotations[i] = new Annotation(
+ Character.toString(hmm.getConsensusAtAlignColumn(i)),
+ description, ' ', value);
+ }
+ information.graphMax = max;
+ // long elapsed = System.currentTimeMillis() - now;
+ // System.out.println(-elapsed);
+ }
+
+ /**
* Derive the gap count annotation row.
*
* @param gaprow
return result;
}
+
/**
* Extract a sorted extract of cDNA codon profile data. The returned array
* contains
for (int col = 0; col < cols; col++)
{
// todo would prefer a Java bean for consensus data
- Hashtable<String, int[]> columnHash = new Hashtable<String, int[]>();
+ Hashtable<String, int[]> columnHash = new Hashtable<>();
// #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
int[] codonCounts = new int[66];
codonCounts[0] = alignment.getSequences().size();
}
return scale;
}
+
+ /**
+ * Returns the information content at a specified column.
+ *
+ * @param column
+ * Index of the column, starting from 0.
+ * @return
+ */
+ public static float getInformationContent(int column,
+ HiddenMarkovModel hmm)
+ {
+ float informationContent = 0f;
+
+ for (char symbol : hmm.getSymbols())
+ {
+ float freq = 0f;
+ freq = ResidueProperties.backgroundFrequencies
+ .get(hmm.getAlphabetType()).get(symbol);
+ Double hmmProb = hmm.getMatchEmissionProbability(column, symbol);
+ float prob = hmmProb.floatValue();
+ informationContent += prob * (Math.log(prob / freq) / Math.log(2));
+
+ }
+
+ return informationContent;
+ }
+
+ /**
+ * Produces a HMM profile for a column in an alignment
+ *
+ * @param aa
+ * Alignment annotation for which the profile is being calculated.
+ * @param column
+ * Column in the alignment the profile is being made for.
+ * @param removeBelowBackground
+ * Boolean indicating whether to ignore residues with probabilities
+ * less than their background frequencies.
+ * @return
+ */
+ public static int[] extractHMMProfile(HiddenMarkovModel hmm, int column,
+ boolean removeBelowBackground)
+ {
+
+ if (hmm != null)
+ {
+ int size = hmm.getNumberOfSymbols();
+ char symbols[] = new char[size];
+ int values[] = new int[size];
+ List<Character> charList = hmm.getSymbols();
+ Integer totalCount = 0;
+
+ for (int i = 0; i < size; i++)
+ {
+ char symbol = charList.get(i);
+ symbols[i] = symbol;
+ int value = getAnalogueCount(hmm, column, symbol,
+ removeBelowBackground);
+ values[i] = value;
+ totalCount += value;
+ }
+
+ QuickSort.sort(values, symbols);
+
+ int[] profile = new int[3 + size * 2];
+
+ profile[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
+ profile[1] = size;
+ profile[2] = 100;
+
+ if (totalCount != 0)
+ {
+ int arrayPos = 3;
+ for (int k = size - 1; k >= 0; k--)
+ {
+ Float percentage;
+ Integer value = values[k];
+ if (removeBelowBackground)
+ {
+ percentage = (value.floatValue() / totalCount.floatValue())
+ * 100;
+ }
+ else
+ {
+ percentage = value.floatValue() / 100f;
+ }
+ int intPercent = Math.round(percentage);
+ profile[arrayPos] = symbols[k];
+ profile[arrayPos + 1] = intPercent;
+ arrayPos += 2;
+ }
+ }
+ return profile;
+ }
+ return null;
+ }
+
+ /**
+ * Converts the emission probability of a residue at a column in the alignment
+ * to a 'count' to allow for processing by the annotation renderer.
+ *
+ * @param hmm
+ * @param column
+ * @param removeBelowBackground
+ * When true, this method returns 0 for any symbols with a match
+ * emission probability less than the background frequency.
+ * @param symbol
+ * @return
+ */
+ static int getAnalogueCount(HiddenMarkovModel hmm, int column,
+ char symbol, boolean removeBelowBackground)
+ {
+ Double value;
+
+ value = hmm.getMatchEmissionProbability(column, symbol);
+ double freq;
+
+ freq = ResidueProperties.backgroundFrequencies
+ .get(hmm.getAlphabetType()).get(symbol);
+ if (value < freq && removeBelowBackground)
+ {
+ return 0;
+ }
+
+ value = value * 10000;
+ return Math.round(value.floatValue());
+ }
}
*/
package jalview.analysis;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
/**
* Store essential properties of a sequence in a hashtable for later recovery
- * Keys are Name, Start, End, SeqFeatures, PdbId
+ * Keys are Name, Start, End, SeqFeatures, PdbId, HMM
*
* @param seq
* SequenceI
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
}
+ if (seq.isHMMConsensusSequence())
+ {
+ sqinfo.put("HMM", seq.getHMM());
+ }
return sqinfo;
}
Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
String description = (String) sqinfo.get("Description");
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
+ HiddenMarkovModel hmm = (HiddenMarkovModel) sqinfo.get("HMM");
if (oldname == null)
{
namePresent = false;
sq.setDatasetSequence(seqds);
}
+ if (hmm != null)
+ {
+ sq.setHMM(new HiddenMarkovModel(hmm));
+ sq.setIsHMMConsensusSequence(true);
+ }
return namePresent;
}
boolean isNormaliseSequenceLogo();
+ boolean isShowInformationHistogram();
+
+ boolean isShowHMMSequenceLogo();
+
+ boolean isNormaliseHMMSequenceLogo();
+
ColourSchemeI getGlobalColourScheme();
/**
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
*
* @return
*/
+ @Override
boolean isProteinFontAsCdna();
/**
*
* @return
*/
+ @Override
void setProteinFontAsCdna(boolean b);
+
+ void setSequenceInformationHashes(List<ProfilesI> info);
+
+ List<ProfilesI> getSequenceInformationHashes();
+
+ ProfilesI getSequenceInformationHash(int index);
+
+ List<AlignmentAnnotation> getInformationAnnotations();
+
+ AlignmentAnnotation getInformationAnnotation(int index);
+
+ void setSequenceInformationHash(ProfilesI info, int index);
+
+ /**
+ * Initiates the information annotation for all uninitiated sequences.
+ */
+ void initInformation();
+
+ /**
+ * Updates all information annotations.
+ *
+ * @param ap
+ */
+ void updateInformation(AlignmentViewPanel ap);
+
}
alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
+ viewport.updateInformation(alignPanel);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.isFollowHighlight());
// TODO implement for applet
}
+ @Override
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return normaliseHMMSequenceLogo;
+ }
+
+
+
}
private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
.toString();
+ private static String HMMER_PATH;
+
/*
* a date formatter using a fixed (rather than the user's) locale;
* this ensures that date properties can be written and re-read successfully
@Override
public synchronized Enumeration<Object> keys()
{
- return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+ return Collections.enumeration(new TreeSet<>(super.keySet()));
}
};
*/
package jalview.bin;
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import javax.swing.UIManager;
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
/**
* Main class for Jalview Application <br>
* <br>
*
* @param args
* open <em>filename</em>
+ * @throws InterruptedException
+ * @throws IOException
*/
public static void main(String[] args)
{
/**
* @param args
+ * @throws InterruptedException
+ * @throws IOException
*/
void doMain(String[] args)
{
}
try
{
- Map<String, Object> vbinding = new HashMap<String, Object>();
+ Map<String, Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
+ nickname + "|" + url);
if (source == null)
{
- source = new Vector<String>();
+ source = new Vector<>();
}
source.addElement(nickname);
}
System.out.println("adding source '" + data + "'");
if (source == null)
{
- source = new Vector<String>();
+ source = new Vector<>();
}
source.addElement(data);
}
}
/**
+ * Inserts a sequence at a point in the alignment.
+ *
+ * @param i
+ * the index of the position the sequence is to be inserted in.
+ */
+ @Override
+ public void insertSequenceAt(int i, SequenceI snew)
+ {
+ synchronized (sequences)
+ {
+ if (sequences.size() > i)
+ {
+ sequences.add(i, snew);
+ return;
+
+ }
+ else
+ {
+ sequences.add(snew);
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+ return;
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
{
hiddenCols = cols;
}
+
+ /**
+ * Returns all HMM consensus sequences. This will not return real sequences
+ * with HMMs. If remove is set to true, the consensus sequences will be
+ * removed from the alignment.
+ */
+ @Override // TODO make this more efficient.
+ public List<SequenceI> getHMMConsensusSequences(boolean remove)
+ {
+ List<SequenceI> seqs = new ArrayList<>();
+ int position = 0;
+ int seqsRemoved = 0;
+ boolean endReached = false;
+
+ while (!endReached)
+ {
+ SequenceI seq = sequences.get(position);
+ if (seq.isHMMConsensusSequence())
+ {
+ if (remove)
+ {
+ sequences.remove(position);
+ seqsRemoved++;
+ seq.setPreviousPosition(seqsRemoved + position - 1);
+ }
+ else
+ {
+ position++;
+ }
+ seqs.add(seq);
+ }
+ else
+ {
+ position++;
+ }
+
+ if (position >= sequences.size())
+ {
+ endReached = true;
+ }
+ }
+ return seqs;
+ }
}
this.calcId = annotation.calcId;
if (annotation.properties != null)
{
- properties = new HashMap<String, String>();
+ properties = new HashMap<>();
for (Map.Entry<String, String> val : annotation.properties.entrySet())
{
properties.put(val.getKey(), val.getValue());
if (annotation.sequenceMapping != null)
{
Integer p = null;
- sequenceMapping = new HashMap<Integer, Annotation>();
+ sequenceMapping = new HashMap<>();
Iterator<Integer> pos = annotation.sequenceMapping.keySet()
.iterator();
while (pos.hasNext())
int epos = sequenceRef.findPosition(endRes);
if (sequenceMapping != null)
{
- Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> newmapping = new HashMap<>();
Iterator<Integer> e = sequenceMapping.keySet().iterator();
while (e.hasNext())
{
{
return;
}
- sequenceMapping = new HashMap<Integer, Annotation>();
+ sequenceMapping = new HashMap<>();
int seqPos;
/**
* properties associated with the calcId
*/
- protected Map<String, String> properties = new HashMap<String, String>();
+ protected Map<String, String> properties = new HashMap<>();
/**
* base colour for line graphs. If null, will be set automatically by
: false;
// TODO build a better annotation element map and get rid of annotations[]
- Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> mapForsq = new HashMap<>();
if (sequenceMapping != null)
{
if (sp2sq != null)
if (mapping != null)
{
Map<Integer, Annotation> old = sequenceMapping;
- Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
+ Map<Integer, Annotation> remap = new HashMap<>();
int index = -1;
for (int mp[] : mapping.values())
{
{
if (properties == null)
{
- properties = new HashMap<String, String>();
+ properties = new HashMap<>();
}
properties.put(property, value);
}
{
return graphMin < graphMax;
}
+
}
AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
public void setHiddenColumns(HiddenColumns cols);
+
+ /**
+ * Returns all HMM consensus sequences.
+ *
+ * @param remove
+ * If true, remove all HMM consensus sequences from the alignment.
+ * @return
+ */
+ public List<SequenceI> getHMMConsensusSequences(boolean remove);
+
+ /**
+ * Insert a sequence at a position in an alignment
+ *
+ * @param i
+ * The idnex of the position.
+ * @param snew
+ * The new sequence.
+ */
+ void insertSequenceAt(int i, SequenceI snew);
+
+
}
*/
public AlignmentOrder(AlignmentI orderFrom)
{
- Order = new ArrayList<SequenceI>();
+ Order = new ArrayList<>();
for (SequenceI seq : orderFrom.getSequences())
{
*/
public AlignmentOrder(SequenceI[] orderFrom)
{
- Order = new ArrayList<SequenceI>(Arrays.asList(orderFrom));
+ Order = new ArrayList<>(Arrays.asList(orderFrom));
}
/**
* alignment, parent group).
*/
AnnotatedCollectionI getContext();
+
}
--- /dev/null
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * stores data for each node in the hmm model
+ * @author TZVanaalten
+ *
+ */
+public class HMMNode
+{
+ //contains the match emissions for each symbol
+ List<Double> matchEmissions = new ArrayList<>();
+ //contains the insert emissions for each symbol
+ List<Double> insertEmissions = new ArrayList<>();
+ //contains the state transitions for each possible transition. These are bm, bi, bd, im, ii, dm and dd in order (0th position in
+ // the array indicates the probability of a bm transition)
+ List<Double> stateTransitions = new ArrayList<>();
+
+ //annotations
+ Integer alignmentColumn = null;
+ char consensusResidue;
+ char referenceAnnotation;
+ char maskValue;
+ char consensusStructure;
+
+ public HMMNode()
+ {
+ }
+
+ public HMMNode(HMMNode node)
+ {
+ matchEmissions = new ArrayList<>(node.getMatchEmissions());
+ insertEmissions = new ArrayList<>(node.getInsertEmissions());
+ stateTransitions = new ArrayList<>(node.getStateTransitions());
+ alignmentColumn = new Integer(node.getAlignmentColumn());
+ consensusResidue = node.getConsensusResidue();
+ referenceAnnotation = node.getReferenceAnnotation();
+ maskValue = node.getMaskValue();
+ consensusStructure = node.getConsensusStructure();
+ }
+
+ public List<Double> getMatchEmissions()
+ {
+ return matchEmissions;
+ }
+
+ public void setMatchEmissions(List<Double> matchEmissionsL)
+ {
+ this.matchEmissions = matchEmissionsL;
+ }
+ public List<Double> getInsertEmissions()
+ {
+ return insertEmissions;
+ }
+
+ public void setInsertEmissions(List<Double> insertEmissionsL)
+ {
+ this.insertEmissions = insertEmissionsL;
+ }
+
+ public List<Double> getStateTransitions()
+ {
+ return stateTransitions;
+ }
+
+ public void setStateTransitions(List<Double> stateTransitionsM)
+ {
+ this.stateTransitions = stateTransitionsM;
+ }
+
+ public Integer getAlignmentColumn()
+ {
+ return alignmentColumn;
+ }
+ public void setAlignmentColumn(int alignmentColumn)
+ {
+ this.alignmentColumn = alignmentColumn;
+ }
+ public char getConsensusResidue()
+ {
+ return consensusResidue;
+ }
+ public void setConsensusResidue(char consensusResidue)
+ {
+ this.consensusResidue = consensusResidue;
+ }
+ public char getReferenceAnnotation()
+ {
+ return referenceAnnotation;
+ }
+ public void setReferenceAnnotation(char referenceAnnotation)
+ {
+ this.referenceAnnotation = referenceAnnotation;
+ }
+ public char getMaskValue()
+ {
+ return maskValue;
+ }
+ public void setMaskValue(char maskValue)
+ {
+ this.maskValue = maskValue;
+ }
+ public char getConsensusStructure()
+ {
+ return consensusStructure;
+ }
+ public void setConsensusStructure(char consensusStructure)
+ {
+ this.consensusStructure = consensusStructure;
+ }
+}
+
+
--- /dev/null
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Data structure which stores a hidden Markov model. Currently contains file
+ * properties as well, not sure whether these should be transferred to the
+ * HMMFile class
+ *
+ * @author TZVanaalten
+ *
+ */
+public class HiddenMarkovModel
+{
+
+
+ // Stores file properties. Do not directly access this field as it contains
+ // only string value - use the getter methods. For example, to find the length
+ // of theHMM, use getModelLength()to return an int value
+ Map<String, String> fileProperties = new HashMap<>();
+
+ // contains all of the symbols used in this model. The index of each symbol
+ // represents its lookup value
+ List<Character> symbols = new ArrayList<>();
+
+ // contains information for each node in the model. The begin node is at index
+ // 0. Node 0 contains average emission probabilities for each symbol
+ List<HMMNode> nodes = new ArrayList<>();
+
+ // contains the HMM node for each alignment column, alignment columns start at
+ // index 0;
+ Map<Integer, Integer> nodeLookup = new HashMap<>();
+
+ // contains the symbol index for each symbol
+ Map<Character, Integer> symbolIndexLookup = new HashMap<>();
+
+ final static String YES = "yes";
+
+ final static String NO = "no";
+
+ // keys for file properties hashmap
+ private final String NAME = "NAME";
+
+ private final String ACCESSION_NUMBER = "ACC";
+
+ private final String DESCRIPTION = "DESC";
+
+ private final String LENGTH = "LENG";
+
+ private final String MAX_LENGTH = "MAXL";
+
+ private final String ALPHABET = "ALPH";
+
+ private final String DATE = "DATE";
+
+ private final String COMMAND_LOG = "COM";
+
+ private final String NUMBER_OF_SEQUENCES = "NSEQ";
+
+ private final String EFF_NUMBER_OF_SEQUENCES = "EFFN";
+
+ private final String CHECK_SUM = "CKSUM";
+
+ private final String GATHERING_THRESHOLDS = "GA";
+
+ private final String TRUSTED_CUTOFFS = "TC";
+
+ private final String NOISE_CUTOFFS = "NC";
+
+ private final String STATISTICS = "STATS";
+
+ private final String COMPO = "COMPO";
+
+ private final String GATHERING_THRESHOLD = "GA";
+
+ private final String TRUSTED_CUTOFF = "TC";
+
+ private final String NOISE_CUTOFF = "NC";
+
+ private final String VITERBI = "VITERBI";
+
+ private final String MSV = "MSV";
+
+ private final String FORWARD = "FORWARD";
+
+ private final String MAP = "MAP";
+
+ private final String REFERENCE_ANNOTATION = "RF";
+
+ private final String CONSENSUS_RESIDUE = "CONS";
+
+ private final String CONSENSUS_STRUCTURE = "CS";
+
+ private final String MASKED_VALUE = "MM";
+
+ public static final int MATCHTOMATCH = 0;
+
+ public static final int MATCHTOINSERT = 1;
+
+ public static final int MATCHTODELETE = 2;
+
+ public static final int INSERTTOMATCH = 3;
+
+ public static final int INSERTTOINSERT = 4;
+
+ public static final int DELETETOMATCH = 5;
+
+ public static final int DELETETODELETE = 6;
+
+ String fileHeader;
+
+ public HiddenMarkovModel()
+ {
+
+ }
+
+ public HiddenMarkovModel(HiddenMarkovModel hmm)
+ {
+ super();
+ this.fileProperties = new HashMap<>(hmm.fileProperties);
+ this.symbols = new ArrayList<>(hmm.symbols);
+ this.nodes = new ArrayList<>(hmm.nodes);
+ this.nodeLookup = new HashMap<>(hmm.nodeLookup);
+ this.symbolIndexLookup = new HashMap<>(
+ hmm.symbolIndexLookup);
+ this.fileHeader = new String(hmm.fileHeader);
+ }
+
+ /**
+ * Gets the file header of the .hmm file this model came from.
+ *
+ * @return
+ */
+ public String getFileHeader()
+ {
+ return fileHeader;
+ }
+
+ /**
+ * Sets the file header of this model.
+ *
+ * @param header
+ */
+ public void setFileHeader(String header)
+ {
+ fileHeader = header;
+ }
+
+ /**
+ * Returns the map containing the matches between nodes and alignment column
+ * indexes.
+ *
+ * @return
+ *
+ */
+ public Map<Integer, Integer> getNodeLookup()
+ {
+ return nodeLookup;
+ }
+
+ /**
+ * Returns the list of symbols used in this hidden Markov model.
+ *
+ * @return
+ */
+ public List<Character> getSymbols()
+ {
+ return symbols;
+ }
+
+ /**
+ * Returns the file properties.
+ *
+ * @return
+ */
+ public Map<String, String> getFileProperties()
+ {
+ return fileProperties;
+ }
+
+ /**
+ * Gets the node in the hidden Markov model at the specified position.
+ *
+ * @param nodeIndex
+ * The index of the node requested. Node 0 optionally contains the
+ * average match emission probabilities across the entire model, and
+ * always contains the insert emission probabilities and state
+ * transition probabilities for the begin node. Node 1 contains the
+ * first node in the HMM that can correspond to a column in the
+ * alignment.
+ * @return
+ */
+ public HMMNode getNode(int nodeIndex)
+ {
+ return getNodes().get(nodeIndex);
+ }
+
+ /**
+ * Sets the list of symbols used in the hidden Markov model to the list
+ * specified.
+ *
+ * @param symbolsL
+ * The list of symbols to which the current list is to be changed.
+ *
+ */
+ public void setSymbols(List<Character> symbolsL)
+ {
+ this.symbols = symbolsL;
+ }
+
+ /**
+ * Returns the name of the sequence alignment on which the HMM is based.
+ *
+ * @return
+ */
+ public String getName()
+ {
+ return fileProperties.get(NAME);
+ }
+
+ /**
+ * Returns the accession number.
+ * @return
+ */
+ public String getAccessionNumber()
+ {
+ return fileProperties.get(ACCESSION_NUMBER);
+ }
+
+ /**
+ * Returns a description of the sequence alignment on which the hidden Markov
+ * model is based.
+ *
+ * @return
+ */
+ public String getDescription()
+ {
+ return fileProperties.get(DESCRIPTION);
+ }
+
+ /**
+ * Returns the length of the hidden Markov model.
+ *
+ * @return
+ */
+ public Integer getLength()
+ {
+ if (fileProperties.get(LENGTH) == null)
+ {
+ return null;
+ }
+ return Integer.parseInt(fileProperties.get(LENGTH));
+ }
+
+ /**
+ * Returns the max instance length within the hidden Markov model.
+ *
+ * @return
+ */
+ public Integer getMaxInstanceLength()
+ {
+ if (fileProperties.get(MAX_LENGTH) == null)
+ {
+ return null;
+ }
+ return Integer.parseInt(fileProperties.get(MAX_LENGTH));
+ }
+
+ /**
+ * Returns the type of symbol alphabet - "amino", "DNA", "RNA" are the
+ * options. Other alphabets may be added.
+ *
+ * @return
+ */
+ public String getAlphabetType()
+ {
+ return fileProperties.get(ALPHABET);
+ }
+
+ /**
+ * Returns the date as a String.
+ *
+ * @return
+ */
+ public String getDate()
+ {
+ return fileProperties.get(DATE);
+ }
+
+ /**
+ * Returns the command line log.
+ *
+ * @return
+ */
+ public String getCommandLineLog()
+ {
+ return fileProperties.get(COMMAND_LOG);
+ }
+
+ /**
+ * Returns the number of sequences on which the HMM was trained.
+ *
+ * @return
+ */
+ public Integer getNumberOfSequences()
+ {
+ if (fileProperties.get(NUMBER_OF_SEQUENCES) == null)
+ {
+ return null;
+ }
+ return Integer.parseInt(fileProperties.get(NUMBER_OF_SEQUENCES));
+ }
+
+ /**
+ * Returns the effective number of sequences on which the HMM was based.
+ *
+ * @param value
+ */
+ public Double getEffectiveNumberOfSequences()
+ {
+ if (fileProperties.get(LENGTH) == null)
+ {
+ return null;
+ }
+ return Double.parseDouble(fileProperties.get(EFF_NUMBER_OF_SEQUENCES));
+ }
+
+ /**
+ * Returns the checksum.
+ *
+ * @return
+ */
+ public Long getCheckSum()
+ {
+ if (fileProperties.get(LENGTH) == null)
+ {
+ return null;
+ }
+ return Long.parseLong(fileProperties.get(CHECK_SUM));
+ }
+
+ /**
+ * Returns the list of nodes in this HMM.
+ *
+ * @return
+ */
+ public List<HMMNode> getNodes()
+ {
+ return nodes;
+ }
+
+ /**
+ * Sets the list of nodes in this HMM to the given list.
+ *
+ * @param nodes
+ * The list of nodes to which the current list of nodes is being
+ * changed.
+ */
+ public void setNodes(List<HMMNode> nodes)
+ {
+ this.nodes = nodes;
+ }
+
+ /**
+ * Gets the match emission probability for a given symbol at a column in the
+ * alignment.
+ *
+ * @param alignColumn
+ * The index of the alignment column, starting at index 0. Index 0
+ * usually corresponds to index 1 in the HMM.
+ * @param symbol
+ * The symbol for which the desired probability is being requested.
+ * @return
+ *
+ */
+ public Double getMatchEmissionProbability(int alignColumn, char symbol)
+ {
+ int symbolIndex;
+ int nodeIndex;
+ Double probability;
+ if (!symbolIndexLookup.containsKey(symbol))
+ {
+ return 0d;
+ }
+ symbolIndex = symbolIndexLookup.get(symbol);
+ if (nodeLookup.containsKey(alignColumn))
+ {
+ nodeIndex = nodeLookup.get(alignColumn);
+ probability = getNode(nodeIndex).getMatchEmissions().get(symbolIndex);
+ return probability;
+ }
+ else
+ {
+ return 0d;
+ }
+
+ }
+
+ /**
+ * Gets the insert emission probability for a given symbol at a column in the
+ * alignment.
+ *
+ * @param alignColumn
+ * The index of the alignment column, starting at index 0. Index 0
+ * usually corresponds to index 1 in the HMM.
+ * @param symbol
+ * The symbol for which the desired probability is being requested.
+ * @return
+ *
+ */
+ public Double getInsertEmissionProbability(int alignColumn, char symbol)
+ {
+ int symbolIndex;
+ int nodeIndex;
+ Double probability;
+ if (!symbolIndexLookup.containsKey(symbol))
+ {
+ return 0d;
+ }
+ symbolIndex = symbolIndexLookup.get(symbol);
+ if (nodeLookup.containsKey(alignColumn))
+ {
+ nodeIndex = nodeLookup.get(alignColumn);
+ probability = getNode(nodeIndex).getInsertEmissions()
+ .get(symbolIndex);
+ return probability;
+ }
+ else
+ {
+ return 0d;
+ }
+
+ }
+
+ /**
+ * Gets the state transition probability for a given symbol at a column in the
+ * alignment.
+ *
+ * @param alignColumn
+ * The index of the alignment column, starting at index 0. Index 0
+ * usually corresponds to index 1 in the HMM.
+ * @param symbol
+ * The symbol for which the desired probability is being requested.
+ * @return
+ *
+ */
+ public Double getStateTransitionProbability(int alignColumn,
+ int transition)
+ {
+ int nodeIndex;
+ Double probability;
+ if (nodeLookup.containsKey(alignColumn))
+ {
+ nodeIndex = nodeLookup.get(alignColumn);
+ probability = getNode(nodeIndex).getStateTransitions()
+ .get(transition);
+ return probability;
+ }
+ else
+ {
+ return 0d;
+ }
+
+ }
+
+ /**
+ * Returns the alignment column linked to the node at the given index.
+ *
+ * @param nodeIndex
+ * The index of the node, starting from index 1. Index 0 is the begin
+ * node, which does not correspond to a column in the alignment.
+ * @return
+ */
+ public Integer getNodeAlignmentColumn(int nodeIndex)
+ {
+ Integer value = nodes.get(nodeIndex).getAlignmentColumn();
+ return value;
+ }
+
+ /**
+ * Returns the consensus residue at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getConsensusResidue(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getConsensusResidue();
+ return value;
+ }
+
+ /**
+ * Returns the consensus at a given alignment column. If the character is
+ * lower case, its emission probability is less than 0.5.
+ *
+ * @param columnIndex
+ * The index of the column in the alignment for which the consensus
+ * is desired. The list of columns starts at index 0.
+ * @return
+ */
+ public char getConsensusAtAlignColumn(int columnIndex)
+ {
+ char mostLikely = '-';
+ if (consensusResidueIsActive())
+ {
+
+ Integer index = findNodeIndex(columnIndex);
+ if (index == null)
+ {
+ return '-';
+ }
+ mostLikely = getNodes().get(index).getConsensusResidue();
+ return mostLikely;
+ }
+ else
+ {
+ double highestProb = 0;
+ for (char character : symbols)
+ {
+ Double prob = getMatchEmissionProbability(columnIndex, character);
+ if (prob > highestProb)
+ {
+ highestProb = prob;
+ mostLikely = character;
+ }
+ }
+ if (highestProb < 0.5)
+ {
+ mostLikely = Character.toLowerCase(mostLikely);
+ }
+ return mostLikely;
+ }
+
+ }
+
+ /**
+ * Returns the reference annotation at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getReferenceAnnotation(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getReferenceAnnotation();
+ return value;
+ }
+
+ /**
+ * Returns the mask value at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getMaskedValue(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getMaskValue();
+ return value;
+ }
+
+ /**
+ * Returns the consensus structure at the specified node.
+ *
+ * @param nodeIndex
+ * The index of the specified node.
+ * @return
+ */
+ public char getConsensusStructure(int nodeIndex)
+ {
+ char value = nodes.get(nodeIndex).getConsensusStructure();
+ return value;
+ }
+
+ /**
+ * Returns the average match emission probability for a given symbol
+ *
+ * @param symbolIndex
+ * The index of the symbol.
+ * @return
+ *
+ */
+ public double getAverageMatchEmission(int symbolIndex)
+ {
+ double value = nodes.get(0).getMatchEmissions().get(symbolIndex);
+ return value;
+ }
+
+ /**
+ * Returns the number of symbols in the alphabet used in this HMM.
+ *
+ * @return
+ */
+ public int getNumberOfSymbols()
+ {
+ return symbols.size();
+ }
+
+ /**
+ * Adds a file property.
+ *
+ * @param key
+ * @param value
+ */
+ public void addFileProperty(String key, String value)
+ {
+ fileProperties.put(key, value);
+ }
+
+ /**
+ * Returns a boolean indicating whether the reference annotation is active.
+ *
+ * @return
+ */
+ public boolean referenceAnnotationIsActive()
+ {
+ String status;
+ status = fileProperties.get(REFERENCE_ANNOTATION);
+ if (status == null)
+ {
+ return false;
+ }
+ switch (status)
+ {
+ case YES:
+ return true;
+ case NO:
+ return false;
+ default:
+ return false;
+ }
+
+ }
+
+ /**
+ * Returns a boolean indicating whether the mask value annotation is active.
+ *
+ * @return
+ */
+ public boolean maskValueIsActive()
+ {
+ String status;
+ status = fileProperties.get(MASKED_VALUE);
+ if (status == null)
+ {
+ return false;
+ }
+ switch (status)
+ {
+ case YES:
+ return true;
+ case NO:
+ return false;
+ default:
+ return false;
+ }
+
+ }
+
+ /**
+ * Returns a boolean indicating whether the consensus residue annotation is
+ * active.
+ *
+ * @return
+ */
+ public boolean consensusResidueIsActive()
+ {
+ String status;
+ status = fileProperties.get(CONSENSUS_RESIDUE);
+ if (status == null)
+ {
+ return false;
+ }
+ switch (status)
+ {
+ case YES:
+ return true;
+ case NO:
+ return false;
+ default:
+ return false;
+ }
+
+ }
+
+ /**
+ * Returns a boolean indicating whether the consensus structure annotation is
+ * active.
+ *
+ * @return
+ */
+ public boolean consensusStructureIsActive()
+ {
+ String status;
+ status = fileProperties.get(CONSENSUS_STRUCTURE);
+ if (status == null)
+ {
+ return false;
+ }
+ switch (status)
+ {
+ case YES:
+ return true;
+ case NO:
+ return false;
+ default:
+ return false;
+ }
+
+ }
+
+ /**
+ * Returns a boolean indicating whether the MAP annotation is active.
+ *
+ * @return
+ */
+ public boolean mapIsActive()
+ {
+ String status;
+ status = fileProperties.get(MAP);
+ if (status == null)
+ {
+ return false;
+ }
+ switch (status)
+ {
+ case YES:
+ return true;
+ case NO:
+ return false;
+ default:
+ return false;
+ }
+
+ }
+
+ /**
+ * Sets the alignment column of the specified node.
+ *
+ * @param nodeIndex
+ *
+ * @param column
+ *
+ */
+ public void setAlignmentColumn(int nodeIndex, int column)
+ {
+ nodes.get(nodeIndex).setAlignmentColumn(column);
+ }
+
+ /**
+ * Sets the reference annotation at a given node.
+ *
+ * @param nodeIndex
+ * @param value
+ */
+ public void setReferenceAnnotation(int nodeIndex, char value)
+ {
+ nodes.get(nodeIndex).setReferenceAnnotation(value);
+ }
+
+ /**
+ * Sets the consensus residue at a given node.
+ *
+ * @param nodeIndex
+ * @param value
+ */
+ public void setConsensusResidue(int nodeIndex, char value)
+ {
+ nodes.get(nodeIndex).setConsensusResidue(value);
+ }
+
+ /**
+ * Sets the consensus structure at a given node.
+ *
+ * @param nodeIndex
+ * @param value
+ */
+ public void setConsensusStructure(int nodeIndex, char value)
+ {
+ nodes.get(nodeIndex).setConsensusStructure(value);
+ }
+
+ /**
+ * Sets the mask value at a given node.
+ *
+ * @param nodeIndex
+ * @param value
+ */
+ public void setMaskValue(int nodeIndex, char value)
+ {
+ nodes.get(nodeIndex).setMaskValue(value);
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getGatheringThreshold()
+ {
+ String value;
+ value = fileProperties.get("GA");
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getNoiseCutoff()
+ {
+ String value;
+ value = fileProperties.get("NC");
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getTrustedCutoff()
+ {
+ String value;
+ value = fileProperties.get("TC");
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getViterbi()
+ {
+ String value;
+ value = fileProperties.get(VITERBI);
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getMSV()
+ {
+ String value;
+ value = fileProperties.get(MSV);
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getForward()
+ {
+ String value;
+ value = fileProperties.get(FORWARD);
+ return value;
+ }
+
+ /**
+ * Sets the activation status of the MAP annotation.
+ *
+ * @param status
+ */
+ public void setMAPStatus(boolean status)
+ {
+ fileProperties.put(MAP, status ? YES : NO);
+ }
+
+ /**
+ * Sets the activation status of the reference annotation.
+ *
+ * @param status
+ */
+ public void setReferenceAnnotationStatus(boolean status)
+ {
+ fileProperties.put(REFERENCE_ANNOTATION, status ? YES : NO);
+ }
+
+ /**
+ * Sets the activation status of the mask value annotation.
+ *
+ * @param status
+ */
+ public void setMaskedValueStatus(boolean status)
+ {
+ fileProperties.put(MASKED_VALUE, status ? YES : NO);
+ }
+
+ /**
+ * Sets the activation status of the consensus residue annotation.
+ *
+ * @param status
+ */
+ public void setConsensusResidueStatus(boolean status)
+ {
+ fileProperties.put(CONSENSUS_RESIDUE, status ? YES : NO);
+ }
+
+ /**
+ * Sets the activation status of the consensus structure annotation.
+ *
+ * @param status
+ */
+ public void setConsensusStructureStatus(boolean status)
+ {
+ fileProperties.put(CONSENSUS_STRUCTURE, status ? YES : NO);
+ }
+
+ /**
+ * Finds the index of the node in a hidden Markov model based on the column in
+ * the alignment
+ *
+ * @param alignmentColumn
+ * The index of the column in the alignment, with the indexes
+ * starting from 0.
+ */
+
+ public Integer findNodeIndex(int alignmentColumn)
+ {
+ Integer index;
+ index = nodeLookup.get(alignmentColumn);
+ return index;
+ }
+
+ /**
+ * Finds the String values of a boolean. "yes" for true and "no" for false.
+ *
+ * @param value
+ * @return
+ */
+ public static String findStringFromBoolean(boolean value)
+ {
+ if (value)
+ {
+ return YES;
+ }
+ else
+ {
+ return NO;
+ }
+ }
+
+
+
+ /**
+ * Returns the consensus sequence based on the most probable symbol at each
+ * position. The sequence is adjusted to match the length of the existing
+ * sequence alignment. Gap characters are used as padding.
+ *
+ * @param length
+ * The length of the longest sequence in the existing alignment.
+ * @return
+ */
+ public Sequence getConsensusSequence()
+ {
+ int start;
+ int end;
+ int modelLength;
+ start = getNodeAlignmentColumn(1);
+ modelLength = getLength();
+ end = getNodeAlignmentColumn(modelLength);
+ char[] sequence = new char[end + 1];
+ for (int index = 0; index < end + 1; index++)
+ {
+ Character character;
+
+ character = getConsensusAtAlignColumn(index);
+
+ if (character == null || character == '-')
+ {
+ sequence[index] = '-';
+ }
+ else
+ {
+ sequence[index] = Character.toUpperCase(character);
+ }
+ }
+
+
+ Sequence seq = new Sequence(getName() + "_HMM", sequence, start,
+ end);
+ return seq;
+ }
+
+
+ /**
+ * Initiates a HMM consensus sequence
+ *
+ * @return A new HMM consensus sequence
+ */
+ public SequenceI initHMMSequence()
+ {
+ Sequence consensus = getConsensusSequence();
+ consensus.setIsHMMConsensusSequence(true);
+ consensus.setHMM(this);
+ return consensus;
+ }
+
+ public int getSymbolIndex(char c)
+ {
+ return symbolIndexLookup.get(c);
+ }
+
+ public void setSymbolIndex(Character c, Integer i)
+ {
+ symbolIndexLookup.put(c, i);
+ }
+
+}
+
private char[] sequence;
+ int previousPosition;
+
String description;
int start;
int end;
+ boolean hasInfo;
+
+ HiddenMarkovModel hmm;
+
+ boolean isHMMConsensusSequence = false;
+
Vector<PDBEntry> pdbIds;
String vamsasId;
this.addPDBId(new PDBEntry(pdb));
}
}
+ if (seq.getHMM() != null)
+ {
+ this.hmm = new HiddenMarkovModel(seq.getHMM());
+ }
}
@Override
{
if (pdbIds == null)
{
- pdbIds = new Vector<PDBEntry>();
+ pdbIds = new Vector<>();
pdbIds.add(entry);
return true;
}
@Override
public List<int[]> getInsertions()
{
- ArrayList<int[]> map = new ArrayList<int[]>();
+ ArrayList<int[]> map = new ArrayList<>();
int lastj = -1, j = 0;
int pos = start;
int seqlen = sequence.length;
{
if (this.annotation == null)
{
- this.annotation = new Vector<AlignmentAnnotation>();
+ this.annotation = new Vector<>();
}
if (!this.annotation.contains(annotation))
{
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)
{
- List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> result = new ArrayList<>();
if (this.annotation != null)
{
for (AlignmentAnnotation ann : annotation)
}
synchronized (dbrefs)
{
- List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> primaries = new ArrayList<>();
DBRefEntry[] tmp = new DBRefEntry[1];
for (DBRefEntry ref : dbrefs)
{
}
}
+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel hmm)
+ {
+ this.hmm = hmm;
+ }
+
+ @Override
+ public void updateHMMMapping()
+ {
+ int node = 1;
+ int column = 0;
+ for (char residue : sequence)
+ {
+ if (!Comparison.isGap(residue))
+ {
+ hmm.setAlignmentColumn(node, column);
+ hmm.getNodeLookup().put(column, node);
+ node++;
+ }
+ else
+ {
+ hmm.getNodeLookup().remove(column);
+ }
+ column++;
+ }
+
+ }
+
+ @Override
+ public boolean isHMMConsensusSequence()
+ {
+ return isHMMConsensusSequence;
+ }
+
+ @Override
+ public void setIsHMMConsensusSequence(boolean isHMMConsensusSequence)
+ {
+ this.isHMMConsensusSequence = isHMMConsensusSequence;
+ }
+
+ @Override
+ public boolean hasHMMAnnotation()
+ {
+ return hasInfo;
+ /*
+ if (annotation == null)
+ {
+ return false;
+ }
+
+ for (AlignmentAnnotation annot : annotation)
+ {
+ if (annot.label.contains("_HMM"))
+ {
+ return true;
+ }
+ }
+ return false;
+ */
+ }
+
+ @Override
+ public void setHasInfo(boolean status)
+ {
+ hasInfo = true;
+ }
+
+ @Override
+ public int getPreviousPosition()
+ {
+ return previousPosition;
+ }
+
+ @Override
+ public void setPreviousPosition(int previousPosition)
+ {
+ this.previousPosition = previousPosition;
+ }
+
}
*/
private boolean ignoreGapsInConsensus = true;
+ private boolean ignoreBelowBackground = true;
+
/**
* consensus calculation property
*/
AlignmentAnnotation conservation = null;
+ AlignmentAnnotation information = null;
+
private boolean showConsensusHistogram;
private AnnotatedCollectionI context;
+ private boolean showHMMSequenceLogo;
+
+ private boolean normaliseHMMSequenceLogo;
+
+ private boolean showInformationHistogram;
+
/**
* Creates a new SequenceGroup object.
*/
showSequenceLogo = seqsel.showSequenceLogo;
normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
showConsensusHistogram = seqsel.showConsensusHistogram;
+ showHMMSequenceLogo = seqsel.showHMMSequenceLogo;
+ normaliseHMMSequenceLogo = seqsel.normaliseHMMSequenceLogo;
+ showInformationHistogram = seqsel.showInformationHistogram;
idColour = seqsel.idColour;
outlineColour = seqsel.outlineColour;
seqrep = seqsel.seqrep;
thresholdTextColour = seqsel.thresholdTextColour;
width = seqsel.width;
ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
+ ignoreBelowBackground = seqsel.ignoreBelowBackground;
if (seqsel.conserve != null)
{
recalcConservation(); // safer than
*/
public boolean recalcConservation(boolean defer)
{
- if (cs == null && consensus == null && conservation == null)
+ if (cs == null && consensus == null && conservation == null
+ && information == null)
{
return false;
}
{
ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
endRes + 1, showSequenceLogo);
+ if (information != null)
+ {
+ HiddenMarkovModel hmm = information.sequenceRef.getHMM();
+
+ ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
+ (endRes + 1) - startRes, startRes, endRes + 1,
+ showHMMSequenceLogo, ignoreBelowBackground);
+ _updateInformationRow(info, sequences.size());
+ upd = true;
+ }
if (consensus != null)
{
_updateConsensusRow(cnsns, sequences.size());
public ProfilesI consensusData = null;
+ public ProfilesI informationData = null;
+
private void _updateConsensusRow(ProfilesI cnsns, long nseq)
{
if (consensus == null)
}
/**
+ * Recalculates the information content on the HMM annotation.
+ *
+ * @param cnsns
+ * @param nseq
+ */
+ private void _updateInformationRow(ProfilesI cnsns, long nseq)
+ {
+ if (information == null)
+ {
+ getInformation();
+ }
+ information.label = "Information for " + getName();
+ information.description = "Percent Identity";
+ informationData = cnsns;
+ // preserve width if already set
+ int aWidth = (information.annotations != null)
+ ? (endRes < information.annotations.length
+ ? information.annotations.length : endRes + 1)
+ : endRes + 1;
+ information.annotations = null;
+ information.annotations = new Annotation[aWidth]; // should be alignment
+ // width
+
+ AAFrequency.completeInformation(information, cnsns, startRes,
+ endRes + 1, ignoreBelowBackground, showSequenceLogo, nseq); // TODO:
+ // setting
+ // container
+ // for
+ // ignoreGapsInInformationCalculation);
+ }
+
+ /**
* @param s
* sequence to either add or remove from group
* @param recalc
}
/**
+ *
+ * @return information content annotation.
+ */
+ public AlignmentAnnotation getInformation()
+ {
+ // TODO get or calculate and get information annotation row for this group
+ int aWidth = this.getWidth();
+ // pointer
+ // possibility
+ // here.
+ if (aWidth < 0)
+ {
+ return null;
+ }
+ if (information == null)
+ {
+ information = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+ 6.25f, AlignmentAnnotation.BAR_GRAPH);
+ information.hasText = true;
+ information.autoCalculated = false;
+ information.groupRef = this;
+ information.label = getName() + "_HMM";
+ information.description = "Information content, measured in bits";
+ }
+ return information;
+ }
+
+ /**
* set this alignmentAnnotation object as the one used to render consensus
* annotation
*
return ignoreGapsInConsensus;
}
+ public void setIgnoreBelowBackground(boolean state)
+ {
+ if (this.ignoreBelowBackground != state)
+ {
+ ignoreBelowBackground = state;
+ }
+ ignoreBelowBackground = state;
+ }
+
+ public boolean getIgnoreBelowBackground()
+ {
+ return true;
+ }
+
/**
* @param showSequenceLogo
* indicates if a sequence logo is shown for consensus annotation
{
return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
}
+
+ public boolean isShowInformationHistogram()
+ {
+ return showInformationHistogram;
+ }
+
+ public void setShowInformationHistogram(boolean state)
+ {
+ if (showInformationHistogram != state && information != null)
+ {
+ this.showInformationHistogram = state;
+ // recalcConservation(); TODO don't know what to do here next
+ }
+ this.showInformationHistogram = state;
+
+ }
+
+ public boolean isShowHMMSequenceLogo()
+ {
+ // TODO Auto-generated method stub
+ return showHMMSequenceLogo;
+ }
+
+ public void setshowHMMSequenceLogo(boolean state)
+ {
+ showHMMSequenceLogo = state;
+
+ }
+
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ // TODO Auto-generated method stub
+ return normaliseHMMSequenceLogo;
+ }
+
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
}
*/
public void setName(String name);
+ public HiddenMarkovModel getHMM();
+
+ public void setHMM(HiddenMarkovModel hmm);
+
/**
* Get the display name
*/
*/
public List<DBRefEntry> getPrimaryDBRefs();
+ public void updateHMMMapping();
+
+ boolean isHMMConsensusSequence();
+
+ void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
+
+ boolean hasHMMAnnotation();
+
+ void setHasInfo(boolean status);
+
+ int getPreviousPosition();
+
+ void setPreviousPosition(int previousPosition);
+
/**
*
* @return BitSet corresponding to index [0,length) where Comparison.isGap()
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.hmmer.HMMAlignThread;
+import jalview.hmmer.HMMBuildThread;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
import java.beans.PropertyChangeEvent;
import java.io.File;
import java.io.FileWriter;
+import java.io.IOException;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Deque;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
+ Map<String, Float> distribution = new HashMap<>(); // temporary
+
public static final int DEFAULT_WIDTH = 700;
public static final int DEFAULT_HEIGHT = 500;
+ boolean autoAlignNewSequences;
+
+
/*
* The currently displayed panel (selected tabbed view if more than one)
*/
ViewportRanges vpRanges;
public AlignViewControllerI avc;
+ /*
+ * The selected HMM for this align frame
+ */
+ HiddenMarkovModel selectedHMM = null;
List<AlignmentPanel> alignPanels = new ArrayList<>();
*/
String fileName = null;
+
/**
* Creates a new AlignFrame object with specific width and height.
*
}
});
buildColourMenu();
+ buildHMMERMenu();
if (Desktop.desktop != null)
{
}
/**
+ * Adds all menu items to the HMMER menu
+ */
+ private void buildHMMERMenu()
+ {
+ hmmerMenu.removeAll();
+
+ hmmerMenu.add(hmmAlign);
+ hmmerMenu.add(hmmBuild);
+ hmmerMenu.add(hmmSearch);
+ }
+
+ /**
* Change the filename and format for the alignment, and enable the 'reload'
* button functionality.
*
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
ap.av.updateStrucConsensus(ap);
+ ap.av.updateInformation(ap);
}
}
showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+ showInformationHistogram.setSelected(av.isShowInformationHistogram());
+ showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
+ normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
ColourMenuHelper.setColourSelected(colourMenu,
av.getGlobalColourScheme());
}
@Override
+ public void hmmBuild_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
+ {
+ new Thread(new HMMBuildThread(this)).start();
+ alignPanel.repaint();
+
+ }
+
+ @Override
+ public void hmmAlign_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
+ {
+ new Thread(new HMMAlignThread(this, true)).start();
+ alignPanel.repaint();
+ }
+
+ @Override
+ public void changeHMMERLocation_actionPerformed(ActionEvent e)
+ {
+ String location = JOptionPane.showInputDialog(
+ MessageManager.getString("label.enter_location"));
+ Cache.setProperty(Preferences.HMMER_PATH, location);
+ }
+
+ @Override
+ public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
+ {
+ autoAlignNewSequences = autoAlignSeqs;
+ alignPanel.repaint();
+ }
+
+ @Override
+ public void hmmSearch_actionPerformed(ActionEvent e)
+ {
+ alignPanel.repaint();
+ }
+
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
@Override
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
if (viewport.hasHiddenColumns())
{
hiddenColumns = new ArrayList<>();
+
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
ArrayList<int[]> hiddenRegions = viewport.getAlignment()
.getHiddenColumns().getHiddenColumnsCopy();
for (int[] region : hiddenRegions)
+
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(true);
}
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(false);
}
*
* @param newAlignment
* true to paste to a new alignment, otherwise add to this.
+ * @throws InterruptedException
+ * @throws IOException
*/
- void paste(boolean newAlignment)
+ void paste(boolean newAlignment) throws IOException, InterruptedException
{
boolean externalPaste = true;
try
System.out.println("Exception whilst pasting: " + ex);
// could be anything being pasted in here
}
-
}
@Override
*
* @param file
* either a filename or a URL string.
+ * @throws InterruptedException
+ * @throws IOException
*/
public void loadJalviewDataFile(String file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
}
if (isAnnotation)
{
-
alignPanel.adjustAnnotationHeight();
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
}
@Override
+ protected void showInformationHistogram_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowInformationHistogram(
+ showInformationHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
+ protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
+ protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ showHMMSequenceLogo.setState(true);
+ viewport.setShowHMMSequenceLogo(true);
+ viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
new CalculationChooser(AlignFrame.this);
}
}
+
+ /**
+ * Sets the status of the HMMER menu
+ *
+ * @param status
+ */
+ public void updateHMMERStatus(boolean status)
+ {
+ hmmerMenu.setEnabled(status);
+ }
+
+ /**
+ * Returns the selected hidden Markov model.
+ *
+ * @return
+ */
+ public HiddenMarkovModel getSelectedHMM()
+ {
+ return selectedHMM;
+ }
+
+ /**
+ * Sets the selected hidden Markov model
+ *
+ * @param selectedHMM
+ */
+ public void setSelectedHMM(HiddenMarkovModel selectedHMM)
+ {
+ this.selectedHMM = selectedHMM;
+ hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
+ + selectedHMM.getName() + "_HMM");
+ hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
+ + selectedHMM.getName() + "_HMM");
+ }
+
+ @Override
+ public void hmmerMenu_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup grp = getViewport().getSelectionGroup();
+ if (grp != null)
+ {
+ hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
+ + grp.getName());
+ }
+ else
+ {
+ hmmBuild.setText(MessageManager.getString("label.hmmbuild")
+ + " from Alignment");
+ }
+ }
+
}
class PrintThread extends Thread
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
+ initInformation();
+
+
String colourProperty = alignment.isNucleotide()
? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
*/
public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
{
- List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ List<SequenceI[]> seqvectors = new ArrayList<>();
for (PDBEntry pdb : pdbEntries)
{
- List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
+ List<SequenceI> choosenSeqs = new ArrayList<>();
for (SequenceI sq : alignment.getSequences())
{
Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
return normaliseSequenceLogo;
}
+
public void setNormaliseSequenceLogo(boolean state)
{
normaliseSequenceLogo = state;
}
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ normaliseHMMSequenceLogo = state;
+ }
+
/**
*
* @return true if alignment characters should be displayed
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
fr.setTransparency(featureSettings.getTransparency());
}
+ @Override
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return normaliseHMMSequenceLogo;
+ }
+
+
+
}
private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
.compile("<");
+
String TOGGLE_LABELSCALE = MessageManager
.getString("label.scale_label_to_column");
if (selectedRow < aa.length)
{
final String label = aa[selectedRow].label;
- if (!aa[selectedRow].autoCalculated)
+ if (!(aa[selectedRow].autoCalculated)
+ && !(label.indexOf("_HMM") > -1))
{
if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
{
}
else if (label.indexOf("Consensus") > -1)
{
+
+
pop.addSeparator();
// av and sequencegroup need to implement same interface for
+
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null)
// can be
// updated.
av.setShowConsensusHistogram(chist.getState());
- ap.alignFrame.setMenusForViewport();
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
// can be
// updated.
av.setShowSequenceLogo(cprof.getState());
- ap.alignFrame.setMenusForViewport();
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
// updated.
av.setShowSequenceLogo(true);
av.setNormaliseSequenceLogo(cprofnorm.getState());
- ap.alignFrame.setMenusForViewport();
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
consclipbrd.addActionListener(this);
pop.add(consclipbrd);
}
+ else if (label.indexOf("_HMM") > -1) // TODO create labels
+ // in message resource
+ // for these
+ {
+ pop.addSeparator();
+ final AlignmentAnnotation aaa = aa[selectedRow];
+
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString(
+ "label.ignore_below_background_frequency"),
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef
+ .getIgnoreBelowBackground()
+ : ap.av.isIgnoreBelowBackground());
+
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (aaa.groupRef != null)
+ {
+ // TODO: pass on reference to ap so the view can be updated.
+ aaa.groupRef.setIgnoreBelowBackground(cbmi.getState());
+ ap.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(cbmi);
+ if (aaa.groupRef != null)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ aa[selectedRow].groupRef.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ aa[selectedRow].groupRef.isShowHMMSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowHMMSequenceLogo(cprofl.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ aa[selectedRow].groupRef.isNormaliseHMMSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef
+ .setNormaliseHMMSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowHMMSequenceLogo(true);
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowHMMSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.updateInformation(ap);
+ av.setShowHMMSequenceLogo(cprof.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseHMMSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowHMMSequenceLogo(true);
+ av.setNormaliseHMMSequenceLogo(cprofnorm.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ }
}
pop.show(this, evt.getX(), evt.getY());
}
if (av.hasHiddenColumns())
{
+
hiddenColumns = av.getAlignment().getHiddenColumns()
.getHiddenColumnsCopy();
+
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
+import jalview.hmmer.HMMAlignThread;
+import jalview.hmmer.HMMBuildThread;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
JMenuItem sequenceFeature = new JMenuItem();
+ JMenuItem hmmBuildGroup = new JMenuItem();
+
JMenuItem textColour = new JMenuItem();
JMenu jMenu1 = new JMenu();
* currently selected sequence (if there is one):
*/
final List<SequenceI> selectedSequence = (seq == null
- ? Collections.<SequenceI> emptyList()
- : Arrays.asList(seq));
+ ? Collections.<SequenceI> emptyList() : Arrays.asList(seq));
+
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
seqHideAnnotationsMenu, selectedSequence);
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
});
add(menuItem);
+ if (sequence.isHMMConsensusSequence())
+ {
+ JMenuItem selectHMM = new JCheckBoxMenuItem();
+ selectHMM.setText(MessageManager.getString("label.select_hmm"));
+ selectHMM.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ selectHMM_actionPerformed(e);
+ }
+ });
+ add(selectHMM);
+
+ JMenuItem hmmAlign = new JCheckBoxMenuItem();
+ hmmAlign.setText(MessageManager.getString("label.hmmalign"));
+ hmmAlign.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlign_actionPerformed(e);
+ }
+ });
+ add(hmmAlign);
+ }
+
if (ap.av.getSelectionGroup() != null
&& ap.av.getSelectionGroup().getSize() > 1)
{
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(),
- reppdb = new Hashtable<String, PDBEntry>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>(),
+ reppdb = new Hashtable<>();
SequenceI sqass = null;
for (SequenceI sq : ap.av.getSequenceSelection())
{
void addFeatureLinks(final SequenceI seq, List<String> links)
{
JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ Map<String, List<String>> linkset = new LinkedHashMap<>();
for (String link : links)
{
* the insertion order, which is the order of the annotations on the
* alignment.
*/
- Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
- Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(annotations), forSequences);
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
- Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
+ Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
for (int sq = 0; sq < seqs.length; sq++)
{
sequenceFeature_actionPerformed();
}
});
+ hmmBuildGroup.setText(MessageManager.getString("label.group_hmmbuild"));
+ hmmBuildGroup.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuildGroup_actionPerformed();
+ }
+ });
jMenu1.setText(MessageManager.getString("label.group"));
pdbStructureDialog.setText(
MessageManager.getString("label.show_pdbstruct_dialog"));
jMenu1.add(displayNonconserved);
}
+ protected void hmmBuildGroup_actionPerformed()
+ {
+ new Thread(new HMMBuildThread(ap.alignFrame)).start();
+ ap.repaint();
+
+ }
+
+ protected void selectHMM_actionPerformed(ActionEvent e)
+ {
+ HiddenMarkovModel hmm = ap.av.getSequenceSelection()[0].getHMM();
+ ap.alignFrame.setSelectedHMM(hmm);
+ }
+
+ protected void hmmAlign_actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.setSelectedHMM(this.sequence.getHMM());
+ new Thread(new HMMAlignThread(ap.alignFrame, true)).start();
+ ap.repaint();
+ }
+
/**
* Constructs the entries for the colour menu
*/
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- SortedMap<String, String> tipEntries = new TreeMap<String, String>();
- final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
candidates, al);
return;
}
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
/*
* assemble dataset sequences, and template new sequence features,
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
--- /dev/null
+package jalview.hmmer;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.Preferences;
+import jalview.gui.SplitFrame;
+import jalview.io.DataSourceType;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
+public class HMMAlignThread implements Runnable
+{
+
+ /**
+ * feature settings from view that job was associated with
+ */
+ protected FeatureRendererSettings featureSettings = null;
+
+ /**
+ * Object containing frequently used commands.
+ */
+ HMMERCommands cmds = new HMMERCommands();
+
+ AlignFrame af;
+
+ AlignmentI alignment;
+
+ AlignmentI dataset;
+
+ List<AlignmentOrder> orders;
+
+ AlignmentView msa;
+
+ HiddenMarkovModel hmm;
+
+ boolean newFrame;
+
+ long barID;
+
+ Map<Integer, SequenceI> hmmSeqs;
+
+ File hmmTemp = null;
+
+ File outTemp = null;
+
+ File inputTemp = null;
+
+ List<AlignmentOrder> allOrders;
+
+ SequenceI[][] allResults;
+
+ /**
+ * Constructor for the HMMAlignThread. If create new frame is set to true, a
+ * new frame will be created.
+ *
+ * @param af
+ * @param createNewFrame
+ */
+ public HMMAlignThread(AlignFrame af, boolean createNewFrame)
+ {
+ this.af = af;
+ alignment = af.getViewport().getAlignment();
+ if (alignment.getDataset() != null)
+ {
+ dataset = alignment.getDataset();
+ }
+ newFrame = createNewFrame;
+ featureSettings = af.getFeatureRenderer().getSettings();
+ }
+
+ /**
+ * Runs the HMMAlignThread: the data on the alignment or group is exported,
+ * then the command is executed in the command line and then the data is
+ * imported and displayed in a new frame (if true). The command is executed
+ * for each segemtn of the alignment.
+ */
+ @Override
+ public void run()
+ {
+ if (af.getSelectedHMM() == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_selected_hmm"));
+ return;
+ }
+ else
+ {
+ hmm = af.getSelectedHMM();
+ }
+ barID = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
+ barID);
+ cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
+
+ // if (!alignment.isAligned())
+ // {
+ // alignment.padGaps();
+ // }
+ prepareAlignment();
+ SequenceI[][] subAlignments = msa.getVisibleContigs('-');
+ allOrders = new ArrayList<>();
+ allResults = new SequenceI[subAlignments.length][];
+ int job = 0;
+ for (SequenceI[] seqs : subAlignments)
+ {
+ cmds.uniquifySequences(seqs);
+ try
+ {
+ createTemporaryFiles();
+ } catch (IOException e2)
+ {
+ e2.printStackTrace();
+ }
+ try
+ {
+ cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
+ hmmTemp.getAbsoluteFile());
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ try
+ {
+ boolean ran = runCommand();
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmalign_failed"));
+ return;
+ }
+ } catch (IOException | InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ try
+ {
+ importData(job);
+ } catch (IOException | InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ job++;
+ }
+
+ displayResults(newFrame);
+
+ af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
+ barID);
+
+ }
+
+ /**
+ * Creates temporary files for exporting and importing the data.
+ *
+ * @throws IOException
+ */
+ private void createTemporaryFiles() throws IOException
+ {
+ hmmTemp = File.createTempFile("hmm", ".hmm");
+ hmmTemp.deleteOnExit();
+ outTemp = File.createTempFile("output", ".sto");
+ outTemp.deleteOnExit();
+ inputTemp = File.createTempFile("input", ".sto");
+ inputTemp.deleteOnExit();
+ }
+
+ /**
+ * Executes the hmmalign command in the command line.
+ *
+ * @return
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ private boolean runCommand() throws IOException, InterruptedException
+ {
+ File file = new File(cmds.HMMERFOLDER + "/hmmalign");
+ if (!file.canExecute())
+ {
+ file = new File(cmds.HMMERFOLDER + "/hmmalign.exe");
+ {
+ if (!file.canExecute())
+ {
+ return false;
+ }
+ }
+ }
+ String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
+ String version = Cache.getProperty("HMMER_VERSION");
+ if (!"3.1b2".equals(version))
+ {
+ command += cmds.ALLCOL;
+ }
+ boolean trim = true;
+ String bool = Cache.getProperty("TRIM_TERMINI");
+ if ("false".equals(bool))
+ {
+ trim = false;
+ }
+ if (trim)
+ {
+ command += cmds.TRIM;
+ }
+ command += " -o " + inputTemp.getAbsolutePath() + cmds.SPACE
+ + hmmTemp.getAbsolutePath() + cmds.SPACE
+ + outTemp.getAbsolutePath();
+ return cmds.runCommand(command);
+ }
+
+ /**
+ * Imports the data from the temporary file to which the output of hmmalign is
+ * directed.
+ *
+ * @param index
+ * The index of the 'job' (or region of an alignment).
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ private void importData(int index)
+ throws IOException, InterruptedException
+ {
+ StockholmFile file = new StockholmFile(inputTemp.getAbsolutePath(),
+ DataSourceType.FILE);
+ SequenceI[] result = file.getSeqsAsArray();
+ AlignmentOrder msaorder = new AlignmentOrder(result);
+ jalview.analysis.AlignmentSorter.recoverOrder(result);
+ jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, result);
+ allOrders.add(msaorder);
+ allResults[index] = result;
+ hmmTemp.delete();
+ outTemp.delete();
+ inputTemp.delete();
+ }
+
+ /**
+ * Gathers the sequences in preparation for the alignment.
+ */
+ private void prepareAlignment()
+ {
+ // hmmSeqs = alignment.getHMMConsensusSequences(true);
+ msa = af.gatherSequencesForAlignment();
+ }
+
+ /**
+ * Displays the results of all 'jobs'.
+ *
+ * @param newFrame
+ */
+ private void displayResults(boolean newFrame)
+ {
+ AlignmentOrder[] arrOrders = allOrders
+ .toArray(new AlignmentOrder[allOrders.size()]);
+ Object[] newview = msa.getUpdatedView(allResults,
+ arrOrders, '-');
+ SequenceI[] alignment = (SequenceI[]) newview[0];
+ HiddenColumns hidden = (HiddenColumns) newview[1];
+ Alignment al = new Alignment(alignment);
+ al.setProperty("Alignment Program", "hmmalign");
+ if (dataset != null)
+ {
+ al.setDataset(dataset);
+ }
+
+ if (newFrame)
+ {
+ displayInNewFrame(al, allOrders, hidden);
+ }
+ }
+
+ /**
+ * Displays the results in a new frame.
+ *
+ * @param al
+ * The alignment containing the results.
+ * @param alorders
+ * The order of the sequences in the alignment on which the jobs were
+ * run.
+ * @param hidden
+ * Hidden columns in the previous alignment.
+ */
+ private void displayInNewFrame(AlignmentI al,
+ List<AlignmentOrder> alorders, HiddenColumns hidden)
+ {
+ AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ // initialise with same renderer settings as in parent alignframe.
+ af.getFeatureRenderer().transferSettings(this.featureSettings);
+
+ if (allOrders.size() > 0)
+ {
+ addSortByMenuItems(af, allOrders);
+ }
+
+ // TODO: refactor retrieve and show as new splitFrame as Desktop method
+
+ /*
+ * If alignment was requested from one half of a SplitFrame, show in a
+ * SplitFrame with the other pane similarly aligned.
+ */
+ AlignFrame requestedBy = this.af;
+ if (requestedBy != null && requestedBy.getSplitViewContainer() != null
+ && requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy) != null)
+ {
+ AlignmentI complement = requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy);
+ String complementTitle = requestedBy.getSplitViewContainer()
+ .getComplementTitle(requestedBy);
+ // becomes null if the alignment window was closed before the alignment
+ // job finished.
+ AlignmentI copyComplement = new Alignment(complement);
+ // todo should this be done by copy constructor?
+ copyComplement.setGapCharacter(complement.getGapCharacter());
+ // share the same dataset (and the mappings it holds)
+ copyComplement.setDataset(complement.getDataset());
+ copyComplement.alignAs(al);
+ if (copyComplement.getHeight() > 0)
+ {
+ af.setTitle(this.af.getTitle());
+ AlignFrame af2 = new AlignFrame(copyComplement,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ af2.setTitle(complementTitle);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ JInternalFrame splitFrame = new SplitFrame(
+ al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+ return;
+ }
+ }
+
+ /*
+ * Not from SplitFrame, or failed to created a complementary alignment
+ */
+ Desktop.addInternalFrame(af, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ /**
+ * Add sort order options to the AlignFrame menus.
+ *
+ * @param af
+ * @param alorders
+ */
+ protected void addSortByMenuItems(AlignFrame af,
+ List<AlignmentOrder> alorders)
+ {
+ // update orders
+ if (alorders.size() == 1)
+ {
+ af.addSortByOrderMenuItem("hmmalign" + " Ordering", alorders.get(0));
+ }
+ else
+ {
+ // construct a non-redundant ordering set
+ List<String> names = new ArrayList<>();
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ String orderName = " Region " + i;
+ int j = i + 1;
+
+ while (j < l)
+ {
+ if (alorders.get(i).equals(alorders.get(j)))
+ {
+ alorders.remove(j);
+ l--;
+ orderName += "," + j;
+ }
+ else
+ {
+ j++;
+ }
+ }
+
+ if (i == 0 && j == 1)
+ {
+ names.add("");
+ }
+ else
+ {
+ names.add(orderName);
+ }
+ }
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ af.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
+ alorders.get(i));
+ }
+ }
+ }
+
+ /**
+ * Runs hmmalign, and waits for the results to be imported before continuing
+ */
+ public void hmmalignWaitTillComplete()
+ {
+ Thread loader = new Thread(this);
+ loader.start();
+
+ while (loader.isAlive())
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ }
+ }
+
+
--- /dev/null
+package jalview.hmmer;
+
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
+import jalview.gui.Preferences;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileLoader;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.util.MessageManager;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.List;
+
+import javax.swing.JOptionPane;
+
+public class HMMBuildThread implements Runnable
+{
+ HMMERCommands cmds = new HMMERCommands();
+ AlignFrame af;
+
+ AlignViewport viewport;
+ AlignmentI alignment;
+ SequenceGroup group;
+
+
+ boolean forGroup = false;
+
+ File hmmTemp = null;
+
+ File stoTemp = null;
+
+ long barID;
+
+ /**
+ * This is used for validation purposes. Do not use!
+ *
+ * @param viewport
+ */
+ public HMMBuildThread(AlignmentI alignment)
+ {
+ this.alignment = alignment;
+ forGroup = false;
+ }
+
+ public HMMBuildThread(AlignFrame af)
+ {
+ this.af = af;
+ if (af.getViewport().getSelectionGroup() != null)
+ {
+ group = af.getViewport().getSelectionGroup();
+ forGroup = true;
+ }
+ viewport = af.getViewport();
+ alignment = viewport.getAlignment();
+
+ }
+
+ /**
+ * Builds a HMM from an alignment, then imports and adds it to the alignment.
+ */
+ @Override
+ public void run()
+ {
+ barID = System.currentTimeMillis();
+ if (af != null)
+ {
+ af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+ barID);
+ }
+ cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
+ if (alignment == null && group == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_sequence_data"));
+ return;
+ }
+ try
+ {
+ hmmTemp = File.createTempFile("hmm", ".hmm");
+ hmmTemp.deleteOnExit();
+ stoTemp = File.createTempFile("output", ".sto");
+ stoTemp.deleteOnExit();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+
+ try
+ {
+ try
+ {
+ SequenceI[] array;
+ List<SequenceI> seqs = alignment
+ .getHMMConsensusSequences(true);
+ cmds.setHmmSeqs(seqs);
+ if (forGroup)
+ {
+ array = group.getSelectionAsNewSequences(alignment);
+ }
+ else
+ {
+ if (!alignment.isAligned())
+ {
+ alignment.padGaps();
+ }
+ array = alignment.getSequencesArray();
+ }
+ if (array.length < 1)
+ {
+ if (af != null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_sequence_data"));
+ }
+ return;
+ }
+ SequenceI[] newArr = new SequenceI[array.length];
+ int index = 0;
+ for (SequenceI seq : array)
+ {
+ newArr[index] = new Sequence(seq);
+ index++;
+ }
+
+ cmds.uniquifySequences(newArr);
+ cmds.exportData(newArr, stoTemp, null, null);
+ jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
+
+ } catch (FileNotFoundException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+
+ }
+ try
+ {
+ boolean ran = runCommand();
+ if (!ran)
+ {
+ if (af != null)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmbuild_failed"));
+ }
+ return;
+ }
+ } catch (IOException | InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ try
+ {
+
+ importData();
+ } catch (IOException | InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } finally
+ {
+ if (af != null)
+ {
+ af.setProgressBar(
+ MessageManager.getString("status.running_hmmbuild"),
+ barID);
+ }
+ }
+ }
+
+
+
+ /**
+ * Executes the hmmbuild command in the command line.
+ *
+ * @return
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ private boolean runCommand() throws IOException, InterruptedException
+ {
+ File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
+ if (!file.canExecute())
+ {
+ file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
+ {
+ if (!file.canExecute())
+ {
+ return false;
+ }
+ }
+ }
+ String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME;
+ if (forGroup)
+ {
+ command += group.getName();
+ }
+ else
+ {
+ String name = null;
+ if (af != null)
+ {
+ name = af.getTitle();
+ }
+ if (name == null || name == "" || name == " " || name == " ")
+ {
+ name = "Alignment";
+ }
+ command += name;
+ }
+ command += cmds.SPACE;
+ if (!alignment.isNucleotide())
+ {
+ command += cmds.FORCEAMINO; // TODO check for rna
+ }
+ else
+ {
+ command += cmds.FORCEDNA;
+ }
+
+ command += hmmTemp.getAbsolutePath()
+ + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
+ return cmds.runCommand(command);
+ }
+
+ /**
+ * Imports the .hmm file produced by hmmbuild.
+ *
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ private void importData() throws IOException, InterruptedException
+ {
+ if (af != null)
+ {
+ cmds.addHMMConsensusSequences(af);
+
+ FileLoader loader = new FileLoader();
+ loader.LoadFileOntoAlignmentWaitTillLoaded(viewport,
+ hmmTemp.getAbsolutePath(), DataSourceType.FILE,
+ FileFormat.HMMER3);
+ }
+ else
+ {
+ HMMFile file = new HMMFile(new FileParse(hmmTemp.getAbsolutePath(),
+ DataSourceType.FILE));
+ alignment.addSequence(file.getSeqsAsArray()[0]);
+ }
+ hmmTemp.delete();
+ stoTemp.delete();
+ }
+
+ /**
+ * Runs hmmbuild, and waits for the results to be imported before continuing
+ */
+ public void hmmbuildWaitTillComplete()
+ {
+ Thread loader = new Thread(this);
+ loader.start();
+
+ while (loader.isAlive())
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.io.HMMFile;
+import jalview.io.StockholmFile;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.util.Hashtable;
+import java.util.List;
+
+/**
+ * Contains multiple commands and methods frequently used to run hmmbuild,
+ * hmmalign and hmmsearch
+ *
+ * @author TZVanaalten
+ *
+ */
+public class HMMERCommands
+{
+ // Path of hmmer binaries directory
+ String HMMERFOLDER = "/Documents/";
+
+ public String JALVIEWDIRECTORY = System.getProperty("user.dir")
+ + "/";
+
+ public final String HMMALIGN = "/hmmalign ";
+
+ public final String HMMBUILD = "/hmmbuild ";
+
+ public final String HMMSEARCH = "/hmmsearch ";
+
+ public String OUTPUTALIGNMENT;
+
+ public final String NAME = "-n ";
+
+ public final String SPACE = " ";
+
+ public final String ALLCOL = "--allcol ";
+
+ public final String TRIM = "--trim ";
+
+ public final String FORCEAMINO = "--amino ";
+
+ public final String FORCEDNA = "--dna ";
+
+ public final String FORCERNA = "--rna ";
+
+ Hashtable hash = new Hashtable();
+
+ List<SequenceI> hmmSeqs;
+
+ /**
+ * Uniquifies the sequences when exporting and stores their details in a
+ * hashtable.
+ *
+ * @param seqs
+ */
+ public void uniquifySequences(SequenceI[] seqs)
+ {
+ hash = jalview.analysis.SeqsetUtils.uniquify(seqs, true);
+ }
+
+ /**
+ * Recover the sequence data lost by uniquifying.
+ *
+ * @param seqs
+ */
+ public void recoverSequenceNames(SequenceI[] seqs)
+ {
+ jalview.analysis.SeqsetUtils.deuniquify(hash, seqs);
+ }
+
+ /**
+ * Runs a command in the command line.
+ *
+ * @param command
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ public boolean runCommand(String command)
+ throws IOException, InterruptedException
+ {
+ try
+ {
+ final Process p = Runtime.getRuntime().exec(command);
+
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ BufferedReader input = new BufferedReader(
+ new InputStreamReader(p.getInputStream()));
+ String line = null;
+
+ try
+ {
+ while ((line = input.readLine()) != null)
+ {
+ System.out.println(line);
+ }
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }).start();
+
+ p.waitFor();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Exports an alignment and/or HMM to the specified file.
+ *
+ * @param alignment
+ * @throws IOException
+ */
+ public void exportData(SequenceI[] seqs,
+ File stoLocation, HiddenMarkovModel hmm, File hmmLocation)
+ throws IOException
+ {
+ if (seqs != null)
+ {
+ StockholmFile file = new StockholmFile(new Alignment(seqs));
+ String output = file.print(seqs, false);
+ PrintWriter writer = new PrintWriter(stoLocation);
+ writer.println(output);
+ writer.close();
+ }
+
+ if (hmm != null)
+ {
+ HMMFile file = new HMMFile(hmm);
+ PrintWriter writer = new PrintWriter(hmmLocation);
+ writer.print(file.print());
+ writer.close();
+ }
+ }
+
+ /**
+ * Adds any HMM sequences removed before submitting the alignment as a job
+ * back into the alignment.
+ *
+ * @param af
+ */
+ public void addHMMConsensusSequences(AlignFrame af)
+ {
+ AlignmentI al = af.getViewport().getAlignment();
+ for (SequenceI seq : hmmSeqs)
+ {
+ Integer position = seq.getPreviousPosition();
+ al.getSequences().add(position, seq);
+ }
+ af.getViewport().setAlignment(al);
+ af.alignPanel.adjustAnnotationHeight();
+ af.getViewport().updateSequenceIdColours();
+ af.buildSortByAnnotationScoresMenu();
+ }
+
+ /**
+ * Returns the list of HMM sequences removed
+ *
+ * @return
+ */
+ public List<SequenceI> getHmmSeqs()
+ {
+ return hmmSeqs;
+ }
+
+ /**
+ * Sets the list of removed HMM sequences
+ *
+ * @param hmmSeqs
+ */
+ public void setHmmSeqs(List<SequenceI> hmmSeqs)
+ {
+ this.hmmSeqs = hmmSeqs;
+ }
+}
*/
protected void initData()
{
- seqs = new Vector<SequenceI>();
- annotations = new Vector<AlignmentAnnotation>();
- seqGroups = new ArrayList<SequenceGroup>();
+ seqs = new Vector<>();
+ annotations = new Vector<>();
+ seqGroups = new ArrayList<>();
parseCalled = false;
}
@Override
public void setSeqs(SequenceI[] s)
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
for (int i = 0; i < s.length; i++)
{
{
if (newickStrings == null)
{
- newickStrings = new Vector<String[]>();
+ newickStrings = new Vector<>();
}
newickStrings.addElement(new String[] { treeName, newickString });
}
{
seqs.add(seq);
}
+
+ /**
+ * Used only for hmmer statistics, so should probably be removed at some
+ * point. TODO remove this
+ *
+ * @return
+ */
+ public Vector<AlignmentAnnotation> getAnnotations()
+ {
+ return annotations;
+ }
+
}
{
return false;
}
+ },
+ HMMER3("HMMER3", "hmm", true, true)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ return new HMMFile(source);
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return new HMMFile();
+ }
};
+
private boolean writable;
private boolean readable;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Profile;
+import jalview.datamodel.Profiles;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
return alignFrame;
}
+ public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
+ String file, DataSourceType sourceType, FileFormatI format)
+ {
+ this.viewport = viewport;
+ this.file = file;
+ this.protocol = sourceType;
+ this.format = format;
+ _LoadAlignmentFileWaitTillLoaded();
+ }
+
+ protected void _LoadAlignmentFileWaitTillLoaded()
+ {
+ Thread loader = new Thread(this);
+ loader.start();
+
+ while (loader.isAlive())
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+
public void updateRecentlyOpened()
{
Vector recent = new Vector();
}
// append to existing alignment
viewport.addAlignment(al, title);
+ if (source instanceof HMMFile)
+ {
+ AlignmentI alignment = viewport.getAlignment();
+ SequenceI seq = alignment
+ .getSequenceAt(alignment.getAbsoluteHeight() - 1);
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg != null)
+ {
+ seq.insertCharAt(0, sg.getStartRes(), '-');
+ seq.insertCharAt(sg.getEndRes() + 1,
+ alignment.getWidth() - sg.getEndRes(), '-');
+ SequenceI topSeq = sg.getSequencesInOrder(alignment)[0];
+ int topIndex = alignment.findIndex(topSeq);
+ alignment.insertSequenceAt(topIndex, seq);
+ sg.setSeqrep(seq);
+ viewport.getSelectionGroup().addSequence(seq, false);
+ }
+ else
+ {
+ alignment.insertSequenceAt(0, seq);
+ }
+ viewport.initInformation();
+ viewport.setSequenceInformationHash(
+ new Profiles(new Profile[1]), 0);
+ viewport.updateInformation(viewport.getAlignPanel());
+ viewport.getAlignPanel().adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ if (viewport.getAlignPanel().alignFrame
+ .getSelectedHMM() == null)
+ {
+ viewport.getAlignPanel().alignFrame
+ .setSelectedHMM(seq.getHMM());
+ }
+
+ }
}
else
{
--- /dev/null
+package jalview.io;
+
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+
+/**
+ * Adds capability to read in and write out HMMER3 files. .
+ *
+ *
+ * @author TZVanaalten
+ *
+ */
+public class HMMFile extends AlignFile
+ implements AlignmentFileReaderI, AlignmentFileWriterI
+{
+ // HMM to store file data
+ private HiddenMarkovModel hmm;
+
+ // number of possible transitions
+ private static final int NUMBER_OF_TRANSITIONS = 7;
+
+ private String NL = "\n";
+
+ //number of symbols in the alphabet used in the hidden Markov model
+ int numberOfSymbols;
+
+ private final String SPACE = " ";
+
+ private final String COMPO = "COMPO";
+
+ private final String EMPTY = "";
+
+ //This is a line that needs to be added to each HMMER� file. It is purely for readability.
+ private static final String TRANSITIONTYPELINE = " m->m m->i m->d i->m i->i d->m d->d";
+
+ /**
+ * Parses immediately.
+ *
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public HMMFile(String inFile, DataSourceType type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * Parses immediately.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public HMMFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * Default constructor, do not use!
+ */
+ public HMMFile()
+ {
+
+ }
+
+ /**
+ * Constructor for HMMFile used for exporting.
+ *
+ * @param hmm
+ * @param exportImmediately
+ */
+ public HMMFile(HiddenMarkovModel markov)
+ {
+ hmm = markov;
+ }
+
+ /**
+ * For testing, do not use.
+ *
+ * @param br
+ */
+ HMMFile(BufferedReader br)
+ {
+ dataIn = br;
+ }
+
+ /**
+ * Returns the HMM produced by reading in a HMMER3 file.
+ *
+ * @return
+ */
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ /**
+ * Sets the HMM used in this file.
+ *
+ * @param model
+ */
+ public void setHMM(HiddenMarkovModel model)
+ {
+ this.hmm = model;
+ }
+
+ /**
+ * Gets the name of the hidden Markov model.
+ *
+ * @return
+ */
+ public String getName()
+ {
+ return hmm.getName();
+ }
+
+ /**
+ * Reads the data from HMM file into the HMM field on this object.
+ *
+ * @throws IOException
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ hmm = new HiddenMarkovModel();
+ parseFileProperties(dataIn);
+ parseModel(dataIn);
+ }
+
+ /**
+ * Reads the data from HMM file into the HMM field on this object.
+ *
+ * @throws IOException
+ */
+
+ public void parse(BufferedReader br) throws IOException
+ {
+ hmm = new HiddenMarkovModel();
+ parseFileProperties(br);
+ parseModel(br);
+ }
+
+
+
+ /**
+ * Imports the file properties from a HMMER3 file.
+ *
+ * @param input
+ * The buffered reader used to read in the file.
+ * @throws IOException
+ */
+ void parseFileProperties(BufferedReader input) throws IOException
+ {
+ boolean readingFile = true;
+ hmm.setFileHeader(input.readLine());
+ String line = input.readLine();
+ while (readingFile)
+ {
+ if (line != null)
+ {
+ Scanner parser = new Scanner(line);
+ String next = parser.next();
+ if ("HMM".equals(next)) // indicates start of HMM data (end of file
+ // properties)
+ {
+ readingFile = false;
+ fillSymbols(parser);
+ numberOfSymbols = hmm.getNumberOfSymbols();
+ }
+ else if ("STATS".equals(next))
+ {
+ parser.next();
+ String key;
+ String value;
+ key = parser.next();
+ value = parser.next() + SPACE + SPACE + parser.next();
+ hmm.addFileProperty(key, value);
+ }
+ else
+ {
+ String key = next;
+ String value = parser.next();
+ while (parser.hasNext())
+ {
+ value = value + SPACE + parser.next();
+ }
+ hmm.addFileProperty(key, value);
+ }
+ parser.close();
+ }
+ line = input.readLine();
+ if (line == null)
+ {
+ readingFile = false;
+ }
+ }
+
+ }
+
+ /**
+ * Parses the model data from the HMMER3 file
+ *
+ * @param input
+ * The buffered reader used to read the file.
+ * @throws IOException
+ */
+ void parseModel(BufferedReader input) throws IOException
+ {
+ String line = input.readLine();
+ int node = 0;
+ while (!"//".equals(line))
+ {
+ hmm.getNodes().add(new HMMNode());
+ String next;
+ Scanner matchReader = new Scanner(line);
+ next = matchReader.next();
+ if (next.equals(COMPO) || node > 0)
+ {
+ // stores match emission line in list
+ List<Double> matches = new ArrayList<>();
+ matches = fillList(matchReader, numberOfSymbols);
+ hmm.getNodes().get(node).setMatchEmissions(matches);
+ if (node > 0)
+ {
+ parseAnnotations(matchReader, node);
+ }
+ }
+ matchReader.close();
+ // stores insert emission line in list
+ line = input.readLine();
+ Scanner insertReader = new Scanner(line);
+ List<Double> inserts = new ArrayList<>();
+ inserts = fillList(insertReader, numberOfSymbols);
+ hmm.getNodes().get(node).setInsertEmissions(inserts);
+ insertReader.close();
+
+ // stores state transition line in list
+ line = input.readLine();
+ Scanner transitionReader = new Scanner(line);
+ List<Double> transitions = new ArrayList<>();
+ transitions = fillList(transitionReader, NUMBER_OF_TRANSITIONS);
+ hmm.getNodes().get(node).setStateTransitions(transitions);
+ transitionReader.close();
+ line = input.readLine();
+ node++;
+ }
+
+ }
+
+ /**
+ * Parses the annotations on the match emission line.
+ *
+ * @param scanner
+ * The scanner which is processing match emission line.
+ * @param index
+ * The index of node which is being scanned.
+ */
+ void parseAnnotations(Scanner scanner, int index)
+ {
+ if (hmm.mapIsActive() && scanner.hasNext())
+ {
+ int column;
+ column = scanner.nextInt();
+ hmm.getNodes().get(index).setAlignmentColumn(column - 1);
+ hmm.getNodeLookup().put(column - 1, index);
+ }
+ else
+ {
+ scanner.next();
+ }
+
+ if (scanner.hasNext())
+ {
+ char consensusR;
+ consensusR = charValue(scanner.next());
+ hmm.getNodes().get(index).setConsensusResidue(consensusR);
+ }
+
+ if (scanner.hasNext())
+ {
+ char reference;
+ reference = charValue(scanner.next());
+ hmm.getNodes().get(index).setReferenceAnnotation(reference);
+ }
+
+ if (scanner.hasNext())
+ {
+ char value;
+ value = charValue(scanner.next());
+ hmm.getNodes().get(index).setMaskValue(value);
+ }
+ if (scanner.hasNext())
+ {
+ char consensusS;
+ consensusS = charValue(scanner.next());
+ hmm.getNodes().get(index).setConsensusStructure(consensusS);
+ }
+ }
+
+
+
+ /**
+ * Fills a list of doubles based on an input line.
+ *
+ * @param input
+ * The scanner for the line containing the data to be transferred to
+ * the list.
+ * @param numberOfElements
+ * The number of elements in the list to be filled.
+ * @return filled list Returns the list of doubles.
+ * @throws IOException
+ */
+ static List<Double> fillList(Scanner input,
+ int numberOfElements) throws IOException
+ {
+ List<Double> list = new ArrayList<>();
+ for (int i = 0; i < numberOfElements; i++)
+ {
+
+ String next = input.next();
+ if (next.contains("*")) // state transitions to or from delete states
+ // occasionally have values of -infinity. These
+ // values are represented by an * in the .hmm
+ // file.
+ {
+ list.add(Double.NEGATIVE_INFINITY);
+ }
+ else
+ {
+ double prob = Double.valueOf(next);
+ prob = Math.pow(Math.E, -prob);
+ list.add(prob);
+ }
+ }
+ if (list.size() < numberOfElements)
+ {
+ throw new IOException("Incomplete data");
+ }
+ return list;
+ }
+
+ /**
+ * Returns a string to be added to the StringBuilder containing the entire
+ * output String.
+ *
+ * @param initialColumnSeparation
+ * The initial whitespace separation between the left side of the
+ * file and first character.
+ * @param columnSeparation
+ * The separation between subsequent data entries.
+ * @param data
+ * The list fo data to be added to the String.
+ * @return
+ */
+ String addData(int initialColumnSeparation,
+ int columnSeparation, List<String> data)
+ {
+ String line = EMPTY;
+ int index = 0;
+ for (String value : data)
+ {
+ if (index == 0)
+ {
+ line += String.format("%" + initialColumnSeparation + "s", value);
+ }
+ else
+ {
+ line += String.format("%" + columnSeparation + "s", value);
+ }
+ index++;
+ }
+ return line;
+ }
+
+ /**
+ * Converts list of characters into a list of Strings.
+ *
+ * @param list
+ * @return Returns the list of Strings.
+ */
+ List<String> charListToStringList(List<Character> list)
+ {
+ List<String> strList = new ArrayList<>();
+ for (char value : list)
+ {
+ String strValue = Character.toString(value);
+ strList.add(strValue);
+ }
+ return strList;
+ }
+
+ /**
+ * Converts a list of doubles into a list of Strings, rounded to the nearest
+ * 5th decimal place.
+ *
+ * @param list
+ * @param noOfDecimals
+ * @return
+ */
+ List<String> doubleListToStringList(List<Double> list)
+ {
+ List<String> strList = new ArrayList<>();
+ for (double value : list)
+ {
+ String strValue;
+ if (value > 0)
+ {
+ strValue = String.format("%.5f", value);
+
+ }
+ else if (value == -0.00000d)
+ {
+ strValue = "0.00000";
+ }
+ else
+ {
+ strValue = "*";
+ }
+
+ strList.add(strValue);
+ }
+ return strList;
+ }
+
+ /**
+ * Converts a primitive array of Strings to a list of Strings.
+ *
+ * @param array
+ * @return
+ */
+ List<String> stringArrayToStringList(String[] array)
+ {
+ List<String> list = new ArrayList<>();
+ for (String value : array)
+ {
+ list.add(value);
+ }
+
+ return list;
+ }
+
+ /**
+ * Returns a string containing the model data.
+ */
+ String getModelAsString()
+ {
+ StringBuffer output = new StringBuffer();
+ String symbolLine = "HMM";
+ List<Character> charSymbols = hmm.getSymbols();
+ List<String> strSymbols;
+ strSymbols = charListToStringList(charSymbols);
+ symbolLine += addData(11, 9, strSymbols);
+ output.append(symbolLine);
+ output.append(NL + TRANSITIONTYPELINE);
+
+ int length = hmm.getLength();
+
+ for (int node = 0; node <= length; node++)
+ {
+ String matchLine;
+ if (node == 0)
+ {
+ matchLine = String.format("%7s", "COMPO");
+ }
+ else
+ {
+ matchLine = String.format("%7s", node);
+ }
+
+ List<String> strMatches;
+ List<Double> doubleMatches;
+ doubleMatches = convertListToLogSpace(
+ hmm.getNode(node).getMatchEmissions());
+ strMatches = doubleListToStringList(doubleMatches);
+ matchLine += addData(10, 9, strMatches);
+
+
+ if (node != 0)
+ {
+ matchLine += SPACE + (hmm.getNodeAlignmentColumn(node) + 1);
+ matchLine += SPACE + hmm.getConsensusResidue(node);
+ matchLine += SPACE + hmm.getReferenceAnnotation(node);
+ if (hmm.getFileHeader().contains("HMMER3/f"))
+ {
+ matchLine += SPACE + hmm.getMaskedValue(node);
+ matchLine += SPACE + hmm.getConsensusStructure(node);
+ }
+
+ }
+
+ output.append(NL + matchLine);
+
+ String insertLine = EMPTY;
+ List<String> strInserts;
+ List<Double> doubleInserts;
+ doubleInserts = convertListToLogSpace(
+ hmm.getNode(node).getInsertEmissions());
+ strInserts = doubleListToStringList(doubleInserts);
+ insertLine += addData(17, 9, strInserts);
+
+ output.append(NL + insertLine);
+
+ String transitionLine = EMPTY;
+ List<String> strTransitions;
+ List<Double> doubleTransitions;
+ doubleTransitions = convertListToLogSpace(
+ hmm.getNode(node).getStateTransitions());
+ strTransitions = doubleListToStringList(doubleTransitions);
+ transitionLine += addData(17, 9, strTransitions);
+
+ output.append(NL + transitionLine);
+ }
+ return output.toString();
+ }
+
+ /**
+ * Returns a String containing the HMM file properties
+ */
+ String getFilePropertiesAsString()
+ {
+ StringBuffer output = new StringBuffer();
+ String line;
+
+ output.append(hmm.getFileHeader());
+
+ line = String.format("%-5s %1s", "NAME", hmm.getName());
+ output.append(NL + line);
+
+ if (hmm.getAccessionNumber() != null)
+ {
+ line = String.format("%-5s %1s", "ACC", hmm.getAccessionNumber());
+ output.append(NL + line);
+ }
+
+ if (hmm.getDescription() != null)
+ {
+ line = String.format("%-5s %1s", "DESC", hmm.getDescription());
+ output.append(NL + line);
+ }
+ line = String.format("%-5s %1s", "LENG", hmm.getLength());
+ output.append(NL + line);
+
+ if (hmm.getMaxInstanceLength() != null)
+ {
+ line = String.format("%-5s %1s", "MAXL", hmm.getMaxInstanceLength());
+ output.append(NL + line);
+ }
+ line = String.format("%-5s %1s", "ALPH", hmm.getAlphabetType());
+ output.append(NL + line);
+
+ boolean status;
+ String statusStr;
+
+ status = hmm.referenceAnnotationIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "RF",
+ statusStr);
+ output.append(NL + line);
+
+ status = hmm.maskValueIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "MM",
+ statusStr);
+ output.append(NL + line);
+
+ status = hmm.consensusResidueIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "CONS",
+ statusStr);
+ output.append(NL + line);
+
+ status = hmm.consensusStructureIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "CS",
+ statusStr);
+ output.append(NL + line);
+
+ status = hmm.mapIsActive();
+ statusStr = HiddenMarkovModel.findStringFromBoolean(status);
+ line = String.format("%-5s %1s", "MAP",
+ statusStr);
+ output.append(NL + line);
+
+
+ if (hmm.getDate() != null)
+ {
+ line = String.format("%-5s %1s", "DATE", hmm.getDate());
+ output.append(NL + line);
+ }
+ if (hmm.getNumberOfSequences() != null)
+ {
+ line = String.format("%-5s %1s", "NSEQ", hmm.getNumberOfSequences());
+ output.append(NL + line);
+ }
+ if (hmm.getEffectiveNumberOfSequences() != null)
+ {
+ line = String.format("%-5s %1s", "EFFN",
+ hmm.getEffectiveNumberOfSequences());
+ output.append(NL + line);
+ }
+ if (hmm.getCheckSum() != null)
+ {
+ line = String.format("%-5s %1s", "CKSUM", hmm.getCheckSum());
+ output.append(NL + line);
+ }
+ if (hmm.getGatheringThreshold() != null)
+ {
+ line = String.format("%-5s %1s", "GA", hmm.getGatheringThreshold());
+ output.append(NL + line);
+ }
+
+ if (hmm.getTrustedCutoff() != null)
+ {
+ line = String.format("%-5s %1s", "TC", hmm.getTrustedCutoff());
+ output.append(NL + line);
+ }
+ if (hmm.getNoiseCutoff() != null)
+ {
+ line = String.format("%-5s %1s", "NC", hmm.getNoiseCutoff());
+ output.append(NL + line);
+ }
+ if (hmm.getMSV() != null)
+ {
+ line = String.format("%-19s %18s", "STATS LOCAL MSV", hmm.getMSV());
+ output.append(NL + line);
+
+ line = String.format("%-19s %18s", "STATS LOCAL VITERBI",
+ hmm.getViterbi());
+ output.append(NL + line);
+
+ line = String.format("%-19s %18s", "STATS LOCAL FORWARD",
+ hmm.getForward());
+ output.append(NL + line);
+ }
+ return output.toString();
+ }
+
+
+ /**
+ * Returns the char value of a single lettered String.
+ *
+ * @param string
+ * @return
+ */
+ char charValue(String string)
+ {
+ char character;
+ character = string.charAt(0);
+ return character;
+
+ }
+
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
+ if (seqs[0].getHMM() != null)
+ {
+ hmm = seqs[0].getHMM();
+ }
+ return print();
+ }
+
+ /**
+ * Prints the .hmm file to a String.
+ *
+ * @return
+ */
+ public String print()
+ {
+ StringBuffer output = new StringBuffer();
+ output.append(getFilePropertiesAsString());
+ output.append(NL);
+ output.append(getModelAsString());
+ output.append(NL + "//");
+ return output.toString();
+ }
+
+ /**
+ * Converts the probabilities contained in a list into log space.
+ *
+ * @param list
+ */
+ List<Double> convertListToLogSpace(List<Double> list)
+ {
+
+ List<Double> convertedList = new ArrayList<>();
+ for (int i = 0; i < list.size(); i++)
+ {
+ double prob = list.get(i);
+ double logProb = -1 * Math.log(prob);
+
+ convertedList.add(logProb);
+ }
+ return convertedList;
+
+
+ }
+
+ /**
+ * Returns the HMM sequence produced by reading a .hmm file.
+ */
+ @Override
+ public SequenceI[] getSeqsAsArray()
+ {
+ SequenceI hmmSeq = hmm.initHMMSequence();
+ SequenceI[] seq = new SequenceI[1];
+ seq[0] = hmmSeq;
+ return seq;
+
+ }
+
+ /**
+ * Fills symbol array and adds each symbol to an index lookup
+ *
+ * @param parser
+ * The scanner scanning the symbol line in the file.
+ */
+ public void fillSymbols(Scanner parser)
+ {
+ int i = 0;
+ while (parser.hasNext())
+ {
+ String strSymbol = parser.next();
+ char[] symbol = strSymbol.toCharArray();
+ hmm.getSymbols().add(symbol[0]);
+ hmm.setSymbolIndex(symbol[0], i);
+ i++;
+ }
+ }
+
+ @Override
+ public void setNewlineString(String newLine)
+ {
+ NL = newLine;
+ }
+
+ @Override
+ public void setExportSettings(AlignExportSettingI exportSettings)
+ {
+
+ }
+
+ @Override
+ public void configureForView(AlignmentViewPanel viewpanel)
+ {
+
+ }
+
+ @Override
+ public boolean hasWarningMessage()
+ {
+ return false;
+ }
+
+ @Override
+ public String getWarningMessage()
+ {
+ return "warning message";
+ }
+
+}
+
reply = FileFormat.ScoreMatrix;
break;
}
+ if (data.startsWith("HMMER3"))
+ {
+ reply = FileFormat.HMMER3;
+ break;
+ }
if (data.startsWith("H ") && !aaIndexHeaderRead)
{
aaIndexHeaderRead = true;
String version;
// String id;
Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+ LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
Regex p, r, rend, s, x;
// Temporary line for processing RNA annotation
// String RNAannot = "";
strucAnn = new Hashtable();
}
- Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+ Vector<AlignmentAnnotation> newStruc = new Vector<>();
parseAnnotationRow(newStruc, type, ns);
for (AlignmentAnnotation alan : newStruc)
{
private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
{
DBRefEntry dbrf = null;
- List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> dbrs = new ArrayList<>();
String seqdb = "Unknown", sdbac = "" + dbr;
int st = -1, en = -1, p;
if ((st = sdbac.indexOf("/")) > -1)
}
}
+
// output annotations
while (i < s.length && s[i] != null)
{
String key = type2id(alAnot[j].label);
boolean isrna = alAnot[j].isValidStruc();
-
if (isrna)
{
// hardwire to secondary structure if there is RNA secondary
for (int k = 0; k < ann.length; k++)
{
seq += outputCharacter(key, k, isrna, ann, s[i]);
- }
+
+ }
out.append(seq);
out.append(newline);
}
out.append(newline);
}
}
+
+
out.append("//");
out.append(newline);
out.append("# STOCKHOLM 1.0");
out.append(newline);
print(getSeqsAsArray(), false);
-
+
out.append("//");
out.append(newline);
return out.toString();
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
protected JMenu webService = new JMenu();
+ protected JMenu hmmerMenu = new JMenu();
+
+ protected JMenuItem hmmAlign = new JMenuItem();
+
+ protected JMenuItem hmmSearch = new JMenuItem();
+
+ protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
+
protected JMenuItem webServiceNoServices;
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
private SequenceAnnotationOrder annotationSortOrder;
private boolean showAutoCalculatedAbove = false;
- private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
private SplitContainerI splitFrame;
private void jbInit() throws Exception
{
initColourMenu();
-
+ initHMMERMenu();
+
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
ActionListener al = new ActionListener()
saveAs_actionPerformed(e);
}
};
-
+
// FIXME getDefaultToolkit throws an exception in Headless mode
KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
| KeyEvent.SHIFT_MASK,
false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
-
+
closeMenuItem.setText(MessageManager.getString("action.close"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
}
};
addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
-
+
JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
JMenu annotationsMenu = new JMenu(
JMenu calculateMenu = new JMenu(
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
+ hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+ String status = Cache.getProperty("HMMER_FUNCTIONING");
+ if ("false".equals(status) || status == null)
+ {
+ hmmerMenu.setEnabled(false);
+ }
+ else
+ {
+ hmmerMenu.setEnabled(true);
+ }
+ hmmerMenu.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmerMenu_actionPerformed(e);
+ }
+ });
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
}
};
addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
-
+
JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.deselect_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
-
+
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
}
};
addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
-
+
JMenuItem grpsFromSelection = new JMenuItem(
MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(new ActionListener()
}
};
addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
-
+
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
}
};
addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
-
+
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
}
};
addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
-
+
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
}
};
addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
-
+
JMenuItem justifyLeftMenuItem = new JMenuItem(
MessageManager.getString("action.left_justify_alignment"));
justifyLeftMenuItem.addActionListener(new ActionListener()
sortGroupMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
}
};
addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
-
+
JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
MessageManager.getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
-
+
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
+
outputTextboxMenu
.setText(MessageManager.getString("label.out_to_textbox"));
+
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem
.setText(MessageManager.getString("label.show_annotations"));
final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
MessageManager.getString("label.sort_annotations_by_label"));
+
sortAnnBySequence.setSelected(
sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
colourTextMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem htmlMenuItem = new JMenuItem(
MessageManager.getString("label.html"));
htmlMenuItem.addActionListener(new ActionListener()
htmlMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem createBioJS = new JMenuItem(
MessageManager.getString("label.biojs_html_export"));
createBioJS.addActionListener(new java.awt.event.ActionListener()
bioJSMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem overviewMenuItem = new JMenuItem(
MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(new ActionListener()
overviewMenuItem_actionPerformed(e);
}
});
-
+
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
}
};
addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
-
+
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
}
};
addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
-
+
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new ActionListener()
{
wrapMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
}
};
addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
-
+
renderGapsMenuItem
.setText(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem_actionPerformed(e);
}
});
-
+
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
showSeqFeatures.setText(
MessageManager.getString("label.show_sequence_features"));
+
showSeqFeatures.addActionListener(new ActionListener()
{
@Override
.setText(MessageManager.getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showDbRefs_actionPerformed(e);
}
-
+
});
showNpFeatsMenuitem.setText(
MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showNpFeats_actionPerformed(e);
}
-
+
});
showGroupConservation
.setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConservation_actionPerformed(e);
}
-
+
});
showGroupConsensus
.setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showGroupConsensus_actionPerformed(e);
}
-
+
});
showConsensusHistogram.setText(
MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showConsensusHistogram_actionPerformed(e);
}
-
+
});
showSequenceLogo
.setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
showSequenceLogo_actionPerformed(e);
}
-
+
});
normaliseSequenceLogo
.setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
normaliseSequenceLogo_actionPerformed(e);
}
-
+
});
applyAutoAnnotationSettings
.setText(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings_actionPerformed(e);
}
});
-
+
ButtonGroup buttonGroup = new ButtonGroup();
final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
MessageManager.getString("label.show_first"));
sortAnnotations_actionPerformed();
}
});
-
+
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
}
};
addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
-
+
JMenuItem annotationColumn = new JMenuItem(
MessageManager.getString("action.select_by_annotation"));
annotationColumn.addActionListener(new ActionListener()
annotationColumn_actionPerformed(e);
}
});
-
+
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
}
};
addMenuActionAndAccelerator(keyStroke, createGroup, al);
-
+
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
}
};
addMenuActionAndAccelerator(keyStroke, unGroup, al);
-
+
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
}
};
addMenuActionAndAccelerator(keyStroke, copy, al);
-
+
cut.setText(MessageManager.getString("action.cut"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
}
};
addMenuActionAndAccelerator(keyStroke, cut, al);
-
+
JMenuItem delete = new JMenuItem(
MessageManager.getString("action.delete"));
delete.addActionListener(new ActionListener()
delete_actionPerformed(e);
}
});
-
+
pasteMenu.setText(MessageManager.getString("action.paste"));
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
@Override
public void actionPerformed(ActionEvent e)
{
- pasteNew_actionPerformed(e);
+ try
+ {
+ pasteNew_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
};
addMenuActionAndAccelerator(keyStroke, pasteNew, al);
-
+
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
@Override
public void actionPerformed(ActionEvent e)
{
- pasteThis_actionPerformed(e);
+ try
+ {
+ pasteThis_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
};
addMenuActionAndAccelerator(keyStroke, pasteThis, al);
-
+
JMenuItem createPNG = new JMenuItem("PNG");
createPNG.addActionListener(new ActionListener()
{
});
createPNG.setActionCommand(
MessageManager.getString("label.save_png_image"));
-
JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
font.addActionListener(new ActionListener()
{
createEPS(null);
}
});
-
+
JMenuItem createSVG = new JMenuItem("SVG");
createSVG.addActionListener(new ActionListener()
{
createSVG(null);
}
});
-
+
JMenuItem loadTreeMenuItem = new JMenuItem(
MessageManager.getString("label.load_associated_tree"));
loadTreeMenuItem.setActionCommand(
loadTreeMenuItem_actionPerformed(e);
}
});
-
+
scaleAbove.setVisible(false);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
scaleAbove.addActionListener(new ActionListener()
.setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
followHighlight_actionPerformed();
}
-
+
});
-
+
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
{
buildTreeSortMenu();
}
-
+
@Override
public void menuDeselected(MenuEvent e)
{
}
-
+
@Override
public void menuCanceled(MenuEvent e)
{
sort.add(sortByAnnotScore);
sort.addMenuListener(new javax.swing.event.MenuListener()
{
-
+
@Override
public void menuCanceled(MenuEvent e)
{
}
-
+
@Override
public void menuDeselected(MenuEvent e)
{
}
-
+
@Override
public void menuSelected(MenuEvent e)
{
showReverse_actionPerformed(true);
}
});
-
+
JMenuItem extractScores = new JMenuItem(
MessageManager.getString("label.extract_scores"));
extractScores.addActionListener(new ActionListener()
});
extractScores.setVisible(true);
// JBPNote: TODO: make gui for regex based score extraction
-
+
// for show products actions see AlignFrame.canShowProducts
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
-
+
runGroovy.setText(MessageManager.getString("label.run_groovy"));
runGroovy.setToolTipText(
MessageManager.getString("label.run_groovy_tip"));
runGroovy_actionPerformed();
}
});
-
+
JMenuItem openFeatureSettings = new JMenuItem(
MessageManager.getString("action.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
fetchSequence_actionPerformed(e);
}
});
-
+
JMenuItem associatedData = new JMenuItem(
MessageManager.getString("label.load_features_annotations"));
associatedData.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- associatedData_actionPerformed(e);
+ try
+ {
+ associatedData_actionPerformed(e);
+ } catch (IOException | InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
});
autoCalculate.setText(
listenToViewSelections_actionPerformed(e);
}
});
-
+
JMenu addSequenceMenu = new JMenu(
MessageManager.getString("label.add_sequences"));
JMenuItem addFromFile = new JMenuItem(
hiddenMarkers_actionPerformed(e);
}
});
-
+
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
}
};
addMenuActionAndAccelerator(keyStroke, invertColSel, al);
-
+
showComplementMenuItem.setVisible(false);
showComplementMenuItem.addActionListener(new ActionListener()
{
showComplement_actionPerformed(showComplementMenuItem.getState());
}
});
-
+
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
@Override
tabbedPane_mousePressed(e);
}
}
-
+
@Override
public void mouseReleased(MouseEvent e)
{
tabbedPane_focusGained(e);
}
});
-
+
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
}
};
addMenuActionAndAccelerator(keyStroke, save, al);
-
+
reload.setEnabled(false);
reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
reload_actionPerformed(e);
}
});
-
+
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
}
};
addMenuActionAndAccelerator(keyStroke, newView, al);
-
+
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
-
+
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
idRightAlign_actionPerformed(e);
}
});
-
+
gatherViews.setEnabled(false);
gatherViews.setText(MessageManager.getString("action.gather_views"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, gatherViews, al);
-
+
expandViews.setEnabled(false);
expandViews.setText(MessageManager.getString("action.expand_views"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
}
};
addMenuActionAndAccelerator(keyStroke, expandViews, al);
-
+
JMenuItem pageSetup = new JMenuItem(
MessageManager.getString("action.page_setup"));
pageSetup.addActionListener(new ActionListener()
selectHighlightedColumns_actionPerformed(actionEvent);
}
};
+ hmmBuild.setText(MessageManager.getString("label.hmmbuild"));
+ hmmBuild.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ hmmBuild_actionPerformed(e);
+ } catch (IOException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ }
+
+ });
+ hmmAlign.setText(MessageManager.getString("label.hmmalign"));
+ hmmAlign.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ hmmAlign_actionPerformed(e);
+ } catch (IOException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (InterruptedException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ }
+
+ });
selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
JMenu autoAnnMenu = new JMenu(
MessageManager.getString("label.autocalculated_annotation"));
-
+
JMenu exportImageMenu = new JMenu(
MessageManager.getString("label.export_image"));
JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(webService);
-
+ alignFrameMenuBar.add(hmmerMenu);
+
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(reload);
fileMenu.add(associatedData);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
-
+
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
editMenu.add(undoMenuItem);
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
-
+
showMenu.add(showAllColumns);
showMenu.add(showAllSeqs);
showMenu.add(showAllhidden);
viewMenu.add(alignmentProperties);
viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
-
+
annotationsMenu.add(annotationPanelMenuItem);
annotationsMenu.addSeparator();
annotationsMenu.add(showAllAlAnnotations);
calculateMenu.add(extractScores);
calculateMenu.addSeparator();
calculateMenu.add(runGroovy);
-
+
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
// selectMenu.add(listenToViewSelections);
}
+ public void hmmerMenu_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ /**
+ * Constructs the entries on the HMMER menu (does not add them to the menu).
+ */
+ protected void initHMMERMenu()
+ {
+ hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
+ hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
+ hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
+ }
+
/**
* Constructs the entries on the Colour menu (but does not add them to the
* menu).
}
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
{
}
+ protected void autoAlignSeqs_actionPerformed(boolean selected)
+ {
+ }
+
+ protected void hmmAlign_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
+ {
+ }
+
+ protected void changeHMMERLocation_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void hmmBuild_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
+ {
+ }
+
+ protected void hmmSearch_actionPerformed(ActionEvent e)
+ {
+ }
+
public void createPNG(java.io.File f)
{
}
}
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
protected void showComplement_actionPerformed(boolean complement)
{
}
+
+ protected void showInformationHistogram_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
+ {
+
+ }
}
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
+import javax.swing.AbstractButton;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
protected JCheckBox rightAlign = new JCheckBox();
- protected JComboBox<String> fontSizeCB = new JComboBox<String>();
+ protected JComboBox<String> fontSizeCB = new JComboBox<>();
- protected JComboBox<String> fontStyleCB = new JComboBox<String>();
+ protected JComboBox<String> fontStyleCB = new JComboBox<>();
- protected JComboBox<String> fontNameCB = new JComboBox<String>();
+ protected JComboBox<String> fontNameCB = new JComboBox<>();
protected JCheckBox showOccupancy = new JCheckBox();
protected JCheckBox scaleProteinToCdna = new JCheckBox();
- protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
+ protected JComboBox<String> gapSymbolCB = new JComboBox<>();
protected JCheckBox wrap = new JCheckBox();
- protected JComboBox<String> sortby = new JComboBox<String>();
+ protected JComboBox<String> sortby = new JComboBox<>();
- protected JComboBox<String> sortAnnBy = new JComboBox<String>();
+ protected JComboBox<String> sortAnnBy = new JComboBox<>();
- protected JComboBox<String> sortAutocalc = new JComboBox<String>();
+ protected JComboBox<String> sortAutocalc = new JComboBox<>();
protected JCheckBox startupCheckbox = new JCheckBox();
protected JCheckBox showConsensLogo = new JCheckBox();
+ protected JCheckBox showInformationHistogram = new JCheckBox();
+
+ protected JCheckBox showHMMLogo = new JCheckBox();
+
protected JCheckBox showDbRefTooltip = new JCheckBox();
protected JCheckBox showNpTooltip = new JCheckBox();
+
/*
* Structure tab and components
*/
protected JCheckBox addTempFactor = new JCheckBox();
- protected JComboBox<String> structViewer = new JComboBox<String>();
+ protected JComboBox<String> structViewer = new JComboBox<>();
protected JTextField chimeraPath = new JTextField();
protected JPanel maxColour = new JPanel();
- protected JComboBox<String> protColour = new JComboBox<String>();
+ protected JComboBox<String> protColour = new JComboBox<>();
- protected JComboBox<String> nucColour = new JComboBox<String>();
+ protected JComboBox<String> nucColour = new JComboBox<>();
/*
* Connections tab components
/*
* Output tab components
*/
- protected JComboBox<Object> epsRendering = new JComboBox<Object>();
+ protected JComboBox<Object> epsRendering = new JComboBox<>();
protected JLabel userIdWidthlabel = new JLabel();
protected JCheckBox sortByTree = new JCheckBox();
/*
+ * hmmer tab and components
+ */
+ protected JPanel hmmerTab = new JPanel();
+
+ protected JCheckBox trimTermini = new JCheckBox();
+
+ protected ButtonGroup backgroundFreqSource = new ButtonGroup();
+
+ protected AbstractButton uniprot = new JCheckBox();
+
+ protected AbstractButton alignment = new JCheckBox();
+
+ protected JLabel sequencesToKeep = new JLabel();
+
+ protected JTextField numberOfSequencesToKeepField = new JTextField();
+
+ protected JLabel installationLocation = new JLabel();
+
+ protected JCheckBox isHMMERInstalled = new JCheckBox();
+
+ protected JTextField hmmerPath = new JTextField();
+
+ protected JLabel hmmsearch = new JLabel();
+
+ protected JLabel hmmalign = new JLabel();
+
+ /*
* DAS Settings tab
*/
protected JPanel dasTab = new JPanel();
*/
protected JPanel wsTab = new JPanel();
+
+
/**
* Creates a new GPreferences object.
*/
tabbedPane.add(initEditingTab(),
MessageManager.getString("label.editing"));
+ tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+
/*
* See DasSourceBrowser for the real work of configuring this tab.
*/
return;
}
}
+ else if (lastTab == hmmerTab
+ && tabbedPane.getSelectedComponent() != hmmerTab
+ && isHMMERInstalled.isSelected())
+ {
+ if (!validateHMMER())
+ {
+ tabbedPane.setSelectedComponent(hmmerTab);
+ }
+ return;
+ }
lastTab = tabbedPane.getSelectedComponent();
}
}
/**
+ * Initialises the hmmer tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initHMMERTab()
+ {
+ hmmerTab.setLayout(null);
+
+ hmmalign.setFont(LABEL_FONT);
+ hmmalign.setText(MessageManager.getString("label.hmmalign_label"));
+ hmmalign.setBounds(new Rectangle(22, 10, 200, 23));
+
+ trimTermini.setFont(LABEL_FONT);
+ trimTermini.setText(MessageManager.getString("label.trim_termini"));
+ trimTermini.setBounds(new Rectangle(22, 30, 200, 23));
+
+ hmmsearch.setFont(LABEL_FONT);
+ hmmsearch.setText(MessageManager.getString("label.hmmsearch_label"));
+ hmmsearch.setBounds(new Rectangle(250, 10, 200, 23));
+
+ sequencesToKeep.setFont(LABEL_FONT);
+ sequencesToKeep
+ .setText(MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setBounds(new Rectangle(250, 30, 125, 23));
+ numberOfSequencesToKeepField.setBounds(new Rectangle(375, 30, 40, 23));
+
+ isHMMERInstalled.setFont(LABEL_FONT);
+ isHMMERInstalled.setText(
+ MessageManager.getString("label.hmmer_installed"));
+ isHMMERInstalled.setBounds(new Rectangle(22, 180, 200, 23));
+ isHMMERInstalled.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ boolean status = isHMMERInstalled.isSelected();
+ installationLocation.setEnabled(status);
+ hmmerPath.setEnabled(status);
+ }
+ });
+ installationLocation.setFont(LABEL_FONT);
+ installationLocation.setText(
+ MessageManager.getString("label.change_hmmer_location"));
+ installationLocation.setBounds(new Rectangle(22, 200, 200, 23));
+ hmmerPath.setBounds(new Rectangle(22, 220, 200, 23));
+ hmmerPath.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser(true);
+ if (chosen != null)
+ {
+ hmmerPath.setText(chosen);
+ }
+ }
+ }
+ });
+
+ backgroundFreqSource.add(uniprot);
+ backgroundFreqSource.add(alignment);
+ backgroundFreqSource.setSelected(uniprot.getModel(), true);
+
+ uniprot.setText(MessageManager.getString("label.freq_uniprot"));
+ uniprot.setFont(LABEL_FONT);
+ uniprot.setBounds(new Rectangle(22, 260, 255, 23));
+
+ alignment.setText(MessageManager.getString("label.freq_alignment"));
+ alignment.setFont(LABEL_FONT);
+ alignment.setBounds(new Rectangle(22, 280, 255, 23));
+
+ hmmerTab.add(uniprot);
+ hmmerTab.add(alignment);
+ hmmerTab.add(hmmalign);
+ hmmerTab.add(hmmsearch);
+ hmmerTab.add(installationLocation);
+ hmmerTab.add(hmmerPath);
+ hmmerTab.add(trimTermini);
+ hmmerTab.add(sequencesToKeep);
+ hmmerTab.add(sequencesToKeep);
+ hmmerTab.add(numberOfSequencesToKeepField);
+ hmmerTab.add(isHMMERInstalled);
+
+ return hmmerTab;
+ }
+
+ /**
* Initialises the Output tabbed panel.
*
* @return
{
if (e.getClickCount() == 2)
{
- String chosen = openFileChooser();
+ String chosen = openFileChooser(false);
if (chosen != null)
{
chimeraPath.setText(chosen);
*
* @return
*/
- protected String openFileChooser()
+ protected String openFileChooser(boolean forFolder)
{
String choice = null;
JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
// chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
return true;
}
+ /**
+ * Validate the hmmer tab preferences; if invalid, set focus on this tab.
+ *
+ * @param e
+ */
+ protected boolean validateHMMER(FocusEvent e)
+ {
+ if (!validateHMMER())
+ {
+ e.getComponent().requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
protected boolean validateStructure()
{
return false;
}
+ protected boolean validateHMMER()
+ {
+ return false;
+ }
+
/**
* Initialises the Visual tabbed panel.
*
}
}
+
+ public void hmmerPath_actionPerformed(ActionEvent e)
+ {
+
+ }
}
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.ProfilesI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.NucleotideColourScheme;
boolean av_renderHistogram = true, av_renderProfile = true,
av_normaliseProfile = false;
+ boolean av_renderInformationHistogram = true, av_renderHMMProfile = true,
+ av_normaliseHMMProfile = false;
+
ResidueShaderI profcolour = null;
private ColumnSelection columnSelection;
private boolean av_ignoreGapsConsensus;
+ private boolean av_ignoreBelowBackground;
+
/**
* attributes set from AwtRenderPanelI
*/
av_renderHistogram = av.isShowConsensusHistogram();
av_renderProfile = av.isShowSequenceLogo();
av_normaliseProfile = av.isNormaliseSequenceLogo();
+ av_renderInformationHistogram = av.isShowInformationHistogram();
+ av_renderHMMProfile = av.isShowHMMSequenceLogo();
+ av_normaliseHMMProfile = av.isNormaliseHMMSequenceLogo();
profcolour = av.getResidueShading();
if (profcolour == null || profcolour.getColourScheme() == null)
{
complementConsensus = av.getComplementConsensusHash();
hStrucConsensus = av.getRnaStructureConsensusHash();
av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
+ av_ignoreBelowBackground = av.isIgnoreBelowBackground();
}
+
+
/**
* Returns profile data; the first element is the profile type, the second is
* the number of distinct values, the third the total count, and the remainder
// properties/rendering attributes as a global 'alignment group' which holds
// all vis settings for the alignment as a whole rather than a subset
//
- if (aa.autoCalculated && (aa.label.startsWith("Consensus")
- || aa.label.startsWith("cDNA Consensus")))
+ if (aa.label.contains("_HMM"))
+ {
+ HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
+ return AAFrequency.extractHMMProfile(hmm, column,
+ av_ignoreBelowBackground); // TODO check if this follows standard
+ // pipeline
+ }
+ if (aa.autoCalculated
+ && (aa.label.startsWith("Consensus") || aa.label
+ .startsWith("cDNA Consensus")))
{
boolean forComplement = aa.label.startsWith("cDNA Consensus");
if (aa.groupRef != null && aa.groupRef.consensusData != null
renderProfile = av_renderProfile;
normaliseProfile = av_normaliseProfile;
}
+ else if (row.label.contains("_HMM"))
+ {
+ renderHistogram = av_renderInformationHistogram;
+ renderProfile = av_renderHMMProfile;
+ normaliseProfile = av_normaliseHMMProfile;
+ }
else
{
renderHistogram = true;
{
colourScheme = cs;
}
+
+ @Override
+ public void setInformation(ProfilesI info)
+ {
+ // TODO Auto-generated method stub
+
+ }
}
public abstract void setConsensus(ProfilesI cons);
+ public abstract void setInformation(ProfilesI info);
+
public abstract boolean conservationApplied();
public abstract void setConservationApplied(boolean conservationApplied);
--- /dev/null
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
+
+public class HMMERColourScheme extends ResidueColourScheme
+{
+
+ AnnotatedCollectionI alignment;
+
+ HiddenMarkovModel hmm;
+
+ boolean peptideSpecific;
+
+ boolean nucleotideSpecific;
+
+ public HMMERColourScheme(HiddenMarkovModel markov)
+ {
+ hmm = markov;
+ }
+ public HMMERColourScheme()
+ {
+
+ }
+
+
+ @Override
+ public Color findColour(char symbol, int position, SequenceI seq,
+ String consensusResidue, float pid)
+ {
+ if (hmm ==null)
+ {
+ return Color.white;
+ }
+ return findColour(symbol, position);
+ }
+
+ /**
+ * Returns the colour at a particular symbol at a column in the alignment.
+ *
+ * @param symbol
+ * @param position
+ * @return Red for an insertion, white for a gap, orange for a negative
+ * information content, white to blue for increasing information
+ * content.
+ */
+ private Color findColour(char symbol, int position)
+ {
+
+ if (Comparison.isGap(symbol))
+ {
+ return Color.white;
+ }
+ if (Character.isLowerCase(symbol))
+ {
+ return new Color(230, 0, 0);
+ }
+ Double prob;
+ prob = hmm.getMatchEmissionProbability(position, symbol);
+ double freq = 0;
+ String alpha = hmm.getAlphabetType();
+ if (!ResidueProperties.backgroundFrequencies.get(alpha).containsKey(symbol))
+ {
+ return Color.white;
+ }
+ else
+ {
+ freq = ResidueProperties.backgroundFrequencies.get(alpha).get(symbol);
+ }
+ if (prob == 0)
+ {
+ return new Color(230, 0, 0);
+ }
+ Double value = Math.log(prob / freq);
+ Color colour = null;
+ if (value > 0)
+ {
+
+ colour = ColorUtils.getGraduatedColour(value.floatValue(), 0,
+ Color.WHITE, 4.52f, Color.blue);
+ }
+ else if (value < 0)
+ {
+ return Color.ORANGE;
+
+ }
+ return colour;
+
+ }
+
+
+
+
+
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI collection,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ List<SequenceI> seqs = collection.getSequences();
+ for (SequenceI seq : seqs)
+ {
+ if (seq.getHMM() != null)
+ {
+ hmm = seq.getHMM();
+ break;
+ }
+ }
+
+ }
+
+
+
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ HiddenMarkovModel markov = null;
+ List<SequenceI> seqs = sg.getSequences();
+ for (SequenceI seq : seqs)
+ {
+ if (seq.getHMM() != null)
+ {
+ markov = seq.getHMM();
+ break;
+ }
+ }
+ HMMERColourScheme colour = new HMMERColourScheme(markov);
+ return colour;
+
+ }
+
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ return true;
+
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+
+ return JalviewColourScheme.HMMER.name();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+
+}
Nucleotide("Nucleotide", NucleotideColourScheme.class),
PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
RNAHelices("RNA Helices", RNAHelicesColour.class),
- TCoffee("T-Coffee Scores", TCoffeeColourScheme.class);
+ TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
+ HMMER("HMMER", HMMERColourScheme.class);
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;
public static final int[] purinepyrimidineIndex;
- public static final Map<String, Integer> aa3Hash = new HashMap<String, Integer>();
+ public static final Map<String, Integer> aa3Hash = new HashMap<>();
- public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
+ public static final Map<String, String> aa2Triplet = new HashMap<>();
- public static final Map<String, String> nucleotideName = new HashMap<String, String>();
+ public static final Map<String, String> nucleotideName = new HashMap<>();
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
- public static final Map<String, String> modifications = new HashMap<String, String>();
+ public static final Map<String, String> modifications = new HashMap<>();
+
+ // residue background frequencies across different alphabets
+ public static final Map<String, Map<Character, Float>> backgroundFrequencies = new HashMap<>();
static
{
/**
* Nucleotide Ambiguity Codes
*/
- public static final Map<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+ public static final Map<String, String[]> ambiguityCodes = new Hashtable<>();
/**
* Codon triplets with additional symbols for unambiguous codons that include
* ambiguity codes
*/
- public static final Hashtable<String, String> codonHash2 = new Hashtable<String, String>();
+ public static final Hashtable<String, String> codonHash2 = new Hashtable<>();
/**
* all ambiguity codes for a given base
*/
- public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
+ public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<>();
static
{
List<String> codesfor = _ambiguityCodes.get(r);
if (codesfor == null)
{
- _ambiguityCodes.put(r, codesfor = new ArrayList<String>());
+ _ambiguityCodes.put(r, codesfor = new ArrayList<>());
}
if (!codesfor.contains(acode.getKey()))
{
}
// Stores residue codes/names and colours and other things
- public static Map<String, Map<String, Integer>> propHash = new Hashtable<String, Map<String, Integer>>();
+ public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
- public static Map<String, Integer> hydrophobic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> hydrophobic = new Hashtable<>();
- public static Map<String, Integer> polar = new Hashtable<String, Integer>();
+ public static Map<String, Integer> polar = new Hashtable<>();
- public static Map<String, Integer> small = new Hashtable<String, Integer>();
+ public static Map<String, Integer> small = new Hashtable<>();
- public static Map<String, Integer> positive = new Hashtable<String, Integer>();
+ public static Map<String, Integer> positive = new Hashtable<>();
- public static Map<String, Integer> negative = new Hashtable<String, Integer>();
+ public static Map<String, Integer> negative = new Hashtable<>();
- public static Map<String, Integer> charged = new Hashtable<String, Integer>();
+ public static Map<String, Integer> charged = new Hashtable<>();
- public static Map<String, Integer> aromatic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> aromatic = new Hashtable<>();
- public static Map<String, Integer> aliphatic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> aliphatic = new Hashtable<>();
- public static Map<String, Integer> tiny = new Hashtable<String, Integer>();
+ public static Map<String, Integer> tiny = new Hashtable<>();
- public static Map<String, Integer> proline = new Hashtable<String, Integer>();
+ public static Map<String, Integer> proline = new Hashtable<>();
static
{
public static Hashtable<String, String> toDssp3State;
static
{
- toDssp3State = new Hashtable<String, String>();
+ toDssp3State = new Hashtable<>();
toDssp3State.put("H", "H");
toDssp3State.put("E", "E");
toDssp3State.put("C", " ");
}
+ static
+ {
+ Map<Character, Float> amino = new HashMap<>();
+ amino.put('A', 0.0826f);
+ amino.put('Q', 0.0393f);
+ amino.put('L', 0.0965f);
+ amino.put('S', 0.0661f);
+ amino.put('R', 0.0553f);
+ amino.put('E', 0.0674f);
+ amino.put('K', 0.0582f);
+ amino.put('T', 0.0535f);
+ amino.put('N', 0.0406f);
+ amino.put('G', 0.0708f);
+ amino.put('M', 0.0241f);
+ amino.put('W', 0.0109f);
+ amino.put('D', 0.0546f);
+ amino.put('H', 0.0227f);
+ amino.put('F', 0.0386f);
+ amino.put('Y', 0.0292f);
+ amino.put('C', 0.0137f);
+ amino.put('I', 0.0593f);
+ amino.put('P', 0.0472f);
+ amino.put('V', 0.0686f);
+ backgroundFrequencies.put("amino", amino);
+
+ }
+
+ // TODO get correct frequencies
+
+ static
+ {
+ Map<Character, Float> dna = new HashMap<>();
+ dna.put('A', 0.25f);
+ dna.put('C', 0.25f);
+ dna.put('T', 0.25f);
+ dna.put('G', 0.25f);
+ backgroundFrequencies.put("DNA", dna);
+
+ }
+
+ static
+ {
+ Map<Character, Float> rna = new HashMap<>();
+ rna.put('A', 0.25f);
+ rna.put('C', 0.25f);
+ rna.put('T', 0.25f);
+ rna.put('G', 0.25f);
+ backgroundFrequencies.put("RNA", rna);
+
+ }
+
public static String getCanonicalAminoAcid(String aA)
{
String canonical = modifications.get(aA);
// / cut here
public static void main(String[] args)
{
- Hashtable<String, Vector<String>> aaProps = new Hashtable<String, Vector<String>>();
+ Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
System.out.println("my %aa = {");
// invert property hashes
for (String pname : propHash.keySet())
Vector<String> aprops = aaProps.get(rname);
if (aprops == null)
{
- aprops = new Vector<String>();
+ aprops = new Vector<>();
aaProps.put(rname, aprops);
}
Integer hasprop = phash.get(rname);
public static List<String> getResidues(boolean forNucleotide,
boolean includeAmbiguous)
{
- List<String> result = new ArrayList<String>();
+ List<String> result = new ArrayList<>();
if (forNucleotide)
{
for (String nuc : nucleotideName.keySet())
--- /dev/null
+package jalview.util;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.io.StockholmFile;
+import jalview.schemes.ResidueProperties;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+import java.util.Scanner;
+import java.util.Vector;
+
+/**
+ * Processes probability data. The file indexes used in this program represent
+ * the index of the location of a family or hmm in their respective files,
+ * starting from 0.
+ *
+ * @author TZVanaalten
+ *
+ */
+public class HMMProbabilityDistributionAnalyser
+{
+ AlignmentAnnotation reference = null;
+
+ Vector<SequenceI> sequences;
+
+ HiddenMarkovModel hmm;
+
+ // contains the raw data produced
+ List<ArrayList<Double>> raw = new ArrayList<>();
+
+ // contains binned data
+ Map<String, Double> binned = new HashMap<>();
+
+ // location of the family file
+ String families = "/media/sf_Shared_Folder/PFAM/Family/SeedFamilies.seed";
+
+ // location of the file containing the family-clan links
+ final static String FAMILIESTOCLAN = "/media/sf_Shared_Folder/PFAM/Family/Clanlinks.dat";
+
+ // location of the HMM file
+ String hmms = "/media/sf_Shared_Folder/PFAM/HMMs/Pfam-A.hmm";
+
+ // suffix for raw file
+ final static String RAW = "/Raw.csv";
+
+ // suffix for binned file
+ final static String BINNED = "/Binned.csv";
+
+ // normalisation scale
+ final static double SCALE = 1;
+
+ // current position in file
+ int currentFilePosition = 0;
+
+ final static String NL = "\n";
+
+ Random generator = new Random();
+
+ // current directory
+ String currentFolder;
+
+ boolean keepRaw = false;
+
+ /**
+ * Sets the working directory.
+ *
+ * @param path
+ */
+ public void setFolder(String path)
+ {
+ currentFolder = path;
+ }
+
+ /**
+ * Moves a buffered reader forward in the file by a certain amount of entries.
+ * Each entry in the file is delimited by '//'.
+ *
+ * @param index
+ * The index of the location in the file.
+ * @param br
+ * @throws IOException
+ */
+ public void moveLocationBy(int index, BufferedReader br)
+ throws IOException
+ {
+ for (int i = 0; i < index; i++)
+ {
+ String line = br.readLine();
+ while (!"//".equals(line))
+ {
+ line = br.readLine();
+
+ }
+ }
+
+ }
+
+ /**
+ * Analyses a specified number of families and then saves the data. Before
+ * analysing the data, the previous saved data will be imported and after
+ * analysing this, the data is exported back into the file. The file must be
+ * in flat file format.
+ *
+ * @param increments
+ * The number of families to read before saving.
+ * @throws IOException
+ */
+ public void run(int increments, boolean keepRawData) throws IOException
+ {
+ keepRaw = keepRawData;
+ try
+ {
+ readPreviousData(currentFolder);
+ BufferedReader posReader = new BufferedReader(
+ new FileReader(currentFolder + "/CurrentPosition.txt"));
+
+ String line = posReader.readLine();
+ posReader.close();
+ currentFilePosition = Integer.parseInt(line);
+ } catch (Exception e)
+ {
+ System.out.println("No previous data found");
+ }
+
+
+
+ BufferedReader inputSTO = new BufferedReader(new FileReader(families));
+ BufferedReader inputHMM = new BufferedReader(new FileReader(hmms));
+
+
+
+ moveLocationBy(currentFilePosition, inputHMM);
+ moveLocationBy(currentFilePosition, inputSTO);
+
+ int filesRead = 0;
+ int i = 0;
+ while (filesRead < increments)
+ {
+
+ readStockholm(inputSTO);
+
+ readHMM(inputHMM);
+
+ int count = countValidResidues();
+ processData(count);
+ filesRead++;
+
+ currentFilePosition++;
+ System.out.println(i);
+ i++;
+ }
+
+ PrintWriter p = new PrintWriter(
+ new File(currentFolder + "/CurrentPosition.txt"));
+ p.print(currentFilePosition);
+ p.close();
+ exportData(currentFolder);
+ raw.clear();
+ binned.clear();
+
+ }
+
+ /**
+ * Analyses all families and then saves the data. Before analysing the data,
+ * the previous saved data will be imported and after analysing this, the data
+ * is exported back into the file. The file must be in flat file format.
+ *
+ * @param increments
+ * The number of families to read before saving.
+ * @throws IOException
+ */
+ public void runToEnd(boolean keepRawData, boolean forClans)
+ throws IOException
+ {
+ keepRaw = keepRawData;
+ BufferedReader inputSTO = null;
+ BufferedReader inputHMM = null;
+ int size = 0;
+ int files = 1;
+ try
+ {
+ if (forClans)
+ {
+ files = 603;
+ }
+ int filesRead = 0;
+ for (int clan = 0; clan < files; clan++)
+ {
+ System.out.println(clan);
+ String clanPath = "";
+ int numberOfFamilies = 0;
+ if (forClans)
+ {
+ clanPath = currentFolder + "/Clan" + clan;
+ if (!new File(clanPath).exists())
+ {
+ continue;
+ }
+ BufferedReader famCountReader = new BufferedReader(
+ new FileReader(clanPath + "/NumberOfFamilies.txt"));
+ numberOfFamilies = Integer.parseInt(famCountReader.readLine());
+ }
+ else
+ {
+ numberOfFamilies = 1;
+ }
+
+ for (int fam = 0; fam < numberOfFamilies; fam++)
+ {
+ if (forClans)
+ {
+ families = clanPath + "/Families/Fam" + fam + ".sto";
+ hmms = clanPath + "/HMMs/HMM" + fam + ".hmm";
+ }
+
+ inputSTO = new BufferedReader(new FileReader(families));
+ inputHMM = new BufferedReader(new FileReader(hmms));
+
+
+ int i = 0;
+ boolean endReached = atEnd(inputSTO);
+ while (!endReached)
+ {
+ readStockholm(inputSTO);
+ readHMM(inputHMM);
+
+ int count = countValidResidues();
+ processData(count);
+ filesRead++;
+ System.out.println(filesRead);
+ endReached = atEnd(inputSTO);
+ }
+ }
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } finally
+ {
+ exportData(currentFolder);
+ raw.clear();
+ binned.clear();
+ }
+ }
+
+ /**
+ * Reads the previous data from both files
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readPreviousData(String source) throws IOException
+ {
+ readBinned(source);
+ if (keepRaw)
+ {
+ readRaw(source);
+ }
+ }
+
+ /**
+ * Reads the previous data from the binned file.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readBinned(String source) throws IOException
+ {
+ BufferedReader input = new BufferedReader(
+ new FileReader(source + BINNED));
+ String line = input.readLine();
+ binned = new HashMap<>();
+ while (!("".equals(line) || line == null))
+ {
+ Scanner scanner = new Scanner(line);
+ scanner.useDelimiter(",");
+ String key = scanner.next();
+ String value = scanner.next();
+ binned.put(key, Double.valueOf(value));
+ scanner.close();
+ line = input.readLine();
+ }
+
+ input.close();
+ }
+
+ /**
+ * Reads the previous data from the raw file.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readRaw(String source) throws IOException
+ {
+ BufferedReader input = new BufferedReader(new FileReader(source + RAW));
+ String line = input.readLine();
+ if (line == null)
+ {
+ input.close();
+ return;
+ }
+ Scanner numberScanner = new Scanner(line);
+ numberScanner.useDelimiter(",");
+ raw = new ArrayList<>();
+ while (numberScanner.hasNext())
+ {
+ numberScanner.next();
+ raw.add(new ArrayList<Double>());
+ }
+ numberScanner.close();
+
+ line = input.readLine();
+ while (!("".equals(line) || line == null))
+ {
+ Scanner scanner = new Scanner(line);
+ scanner.useDelimiter(",");
+
+ int i = 0;
+ while (scanner.hasNext())
+ {
+ String value;
+ value = scanner.next();
+ if (!value.equals("EMPTY"))
+ {
+ raw.get(i).add(Double.parseDouble(value));
+ }
+ else
+ {
+ raw.get(i).add(null);
+ }
+
+ i++;
+ }
+ scanner.close();
+ line = input.readLine();
+ }
+
+ input.close();
+ }
+
+ /**
+ * Counts the number of valid residues in the sequence.
+ *
+ * @return
+ */
+ public int countValidResidues()
+ {
+ int count = 0;
+
+ for (int width = 0; width < sequences.size(); width++)
+ {
+ for (int length = 1; length < hmm.getLength() + 1; length++)
+ {
+ char symbol;
+ int alignPos;
+ alignPos = hmm.getNodeAlignmentColumn(length);
+
+ symbol = sequences.get(width).getCharAt(alignPos);
+ if (ResidueProperties.backgroundFrequencies.get("amino")
+ .containsKey(symbol))
+ {
+ count++;
+ }
+ }
+ }
+
+ return count;
+ }
+
+ /**
+ * Processes data, and stores it in both a raw and binned format.
+ *
+ * @param count
+ */
+ public void processData(int count)
+ {
+ int rawPos = 0;
+ if (keepRaw)
+ {
+ raw.add(new ArrayList<Double>());
+ rawPos = raw.size() - 1;
+ }
+ Double total = 0d;
+ for (int width = 0; width < sequences.size(); width++)
+ {
+ for (int length = 1; length < hmm.getLength() + 1; length++)
+ {
+ char symbol;
+ int alignPos;
+ alignPos = hmm.getNodeAlignmentColumn(length);
+
+ symbol = sequences.get(width).getCharAt(alignPos);
+ if (ResidueProperties.backgroundFrequencies.get("amino")
+ .containsKey(symbol))
+ {
+ Double prob;
+ Float bfreq;
+ Double llr;
+ prob = hmm.getMatchEmissionProbability(alignPos, symbol);
+ bfreq = ResidueProperties.backgroundFrequencies.get("amino")
+ .get(symbol);
+ if (prob == 0 || bfreq == 0)
+ {
+ System.out.println("error");
+ }
+ llr = Math.log(prob / bfreq);
+ if (keepRaw)
+ {
+ raw.get(rawPos).add(llr);
+ }
+
+ String output;
+ output = String.format("%.1f", llr);
+ total += Double.parseDouble(output);
+ if ("-0.0".equals(output))
+ {
+ output = "0.0";
+ }
+ if (binned.containsKey(output))
+ {
+ double prev = binned.get(output);
+ prev += (SCALE / count);
+ binned.put(output, prev);
+
+ }
+ else
+ {
+ binned.put(output, SCALE / count);
+ }
+ }
+ }
+ }
+ System.out.println(total / count);
+ }
+
+
+ /**
+ * Reads in the sequence data from a Stockholm file.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readStockholm(BufferedReader inputSTO) throws IOException
+ {
+ FileParse parserSTO = new FileParse(inputSTO, "", DataSourceType.FILE);
+ StockholmFile file = new StockholmFile(parserSTO);
+ Vector<AlignmentAnnotation> annots = file.getAnnotations();
+
+ for (AlignmentAnnotation annot : annots)
+ {
+ if (annot.label.contains("Reference"))
+ {
+ reference = annot;
+ }
+ }
+ sequences = file.getSeqs();
+ }
+
+ /**
+ * Reads in the HMM data from a HMMer file.
+ *
+ * @param source
+ * @throws IOException
+ */
+ public void readHMM(BufferedReader inputHMM) throws IOException
+ {
+ FileParse parserHMM = new FileParse(inputHMM, "", DataSourceType.FILE);
+ HMMFile file = new HMMFile(parserHMM);
+ hmm = file.getHMM();
+
+
+ }
+
+ /**
+ * Exports both the binned and raw data into separate files.
+ *
+ * @param location
+ * @throws FileNotFoundException
+ */
+ public void exportData(String location) throws FileNotFoundException
+ {
+ PrintWriter writerBin = new PrintWriter(new File(location + BINNED));
+ for (Map.Entry<String, Double> entry : binned.entrySet())
+ {
+ writerBin.println(entry.getKey() + "," + entry.getValue());
+ }
+ writerBin.close();
+ if (keepRaw)
+ {
+
+ PrintWriter writerRaw = new PrintWriter(new File(location + RAW));
+
+ StringBuilder identifier = new StringBuilder();
+
+ for (int i = 1; i < raw.size() + 1; i++)
+ {
+ identifier.append("Fam " + i + ",");
+ }
+
+ writerRaw.println(identifier);
+
+ boolean rowIsEmpty = false;
+ int row = 0;
+ while (!rowIsEmpty)
+ {
+ rowIsEmpty = true;
+ StringBuilder string = new StringBuilder();
+ for (int column = 0; column < raw.size(); column++)
+ {
+ if (raw.get(column).size() <= row)
+ {
+ string.append("EMPTY,");
+ }
+ else
+ {
+ string.append(raw.get(column).get(row) + ",");
+ rowIsEmpty = false;
+ }
+ }
+ row++;
+ writerRaw.println(string);
+ }
+ writerRaw.close();
+
+ }
+
+ }
+
+ /**
+ * Prints the specified family on the console.
+ *
+ * @param index
+ * @throws IOException
+ */
+ public void printFam(int index) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(families));
+
+ moveLocationBy(index, br);
+
+ String line = br.readLine();
+
+ while (!"//".equals(line))
+ {
+ System.out.println(line);
+ line = br.readLine();
+ }
+ System.out.println(line);
+ br.close();
+
+ }
+
+ /**
+ * Prints the specified HMM on the console.
+ *
+ * @param index
+ * @throws IOException
+ */
+ public void printHMM(int index) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(hmms));
+
+ moveLocationBy(index, br);
+
+ String line = br.readLine();
+
+ while (!"//".equals(line))
+ {
+ System.out.println(line);
+ line = br.readLine();
+ }
+ System.out.println(line);
+ br.close();
+
+ }
+
+ /**
+ * Prints the specified family to a .sto file.
+ *
+ * @param index
+ * @throws IOException
+ */
+ public void exportFam(int index, String location) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(families));
+
+ moveLocationBy(index, br);
+
+ String line = br.readLine();
+ PrintWriter writer = new PrintWriter(
+ new FileOutputStream(new File(location), true));
+ while (!"//".equals(line))
+ {
+ writer.println(line);
+ line = br.readLine();
+ }
+ writer.println(line);
+ writer.close();
+ br.close();
+
+ }
+
+ public void exportFile(BufferedReader br, String location, boolean append)
+ throws IOException
+ {
+ String line = br.readLine();
+ PrintWriter writer = new PrintWriter(
+ new FileOutputStream(location, append));
+ while (!"//".equals(line))
+ {
+ writer.println(line);
+ line = br.readLine();
+ }
+ writer.println(line);
+ writer.close();
+
+
+ }
+
+ public String getHMMName(int index) throws IOException
+ {
+ String name;
+
+ BufferedReader nameFinder = new BufferedReader(new FileReader(hmms));
+
+ moveLocationBy(index, nameFinder);
+
+ nameFinder.readLine();
+
+ Scanner scanner = new Scanner(nameFinder.readLine());
+ name = scanner.next();
+ name = scanner.next();
+ scanner.close();
+ return name;
+ }
+
+ public String getFamilyName(int index) throws IOException
+ {
+ String name;
+
+ BufferedReader nameFinder = new BufferedReader(
+ new FileReader(families));
+
+ moveLocationBy(index, nameFinder);
+
+ nameFinder.readLine();
+
+ Scanner scanner = new Scanner(nameFinder.readLine());
+ name = scanner.next();
+ name = scanner.next();
+ name = scanner.next();
+ scanner.close();
+ return name;
+ }
+
+ /**
+ * Prints the specified family to a .hmm file.
+ *
+ * @param index
+ * @throws IOException
+ */
+ public void exportHMM(int index, String location) throws IOException
+ {
+
+
+ BufferedReader br = new BufferedReader(new FileReader(hmms));
+
+ moveLocationBy(index, br);
+
+ String line = br.readLine();
+
+ PrintWriter writer = new PrintWriter(
+ new FileOutputStream(new File(location), true));
+ while (!"//".equals(line))
+ {
+ writer.println(line);
+ line = br.readLine();
+ }
+ writer.println(line);
+ writer.close();
+ br.close();
+
+ }
+
+ /**
+ * Clears all raw, binned and current position data in the current directory.
+ *
+ * @throws FileNotFoundException
+ */
+ public void clear() throws FileNotFoundException
+ {
+ PrintWriter pos = new PrintWriter(
+ currentFolder + "/CurrentPosition.txt");
+ pos.println("0");
+
+ PrintWriter raw = new PrintWriter(currentFolder + RAW);
+
+ PrintWriter bin = new PrintWriter(currentFolder + BINNED);
+
+ pos.close();
+ bin.close();
+ raw.close();
+ }
+
+ public void sortIntoClans(String directory) throws IOException
+ {
+ BufferedReader clanFinder = new BufferedReader(new FileReader(FAMILIESTOCLAN));
+ BufferedReader familyReader = new BufferedReader(
+ new FileReader(families));
+ BufferedReader hmmReader = new BufferedReader(new FileReader(hmms));
+ int families = 0;
+ // moveLocationBy(7000, familyReader);
+ // moveLocationBy(7000, clanFinder);
+ // moveLocationBy(7000, hmmReader);
+ HashMap<String, Integer> clanIndexes = new HashMap<>();
+ ArrayList<Integer> familyCounts = new ArrayList<>();
+ int filePos = 0;
+ int clanCount = 0;
+ String line;
+ line = clanFinder.readLine();
+
+ while (!"".equals(line) && !" ".equals(line) && line != null)
+ {
+ String clanName;
+ boolean inClan = false;
+ while (!(line.indexOf("//") > -1))
+ {
+
+ if (line.indexOf("#=GF CL") > -1)
+ {
+ families++;
+ System.out.println(families);
+ inClan = true;
+ Scanner scanner = new Scanner(line);
+ scanner.next();
+ scanner.next();
+ clanName = scanner.next();
+ scanner.close();
+
+ if (!clanIndexes.containsKey(clanName))
+ {
+ clanIndexes.put(clanName, clanCount);
+ clanCount++;
+ familyCounts.add(0);
+ }
+
+
+ Integer clanI = clanIndexes.get(clanName);
+ String clanPath = directory + "/Clan" + clanI.toString();
+ createFolders(clanPath);
+
+ int index = clanIndexes.get(clanName);
+ exportFile(familyReader,
+ clanPath + "/Families/Fam" + familyCounts.get(index)
+ + ".sto",
+ false);
+ exportFile(hmmReader,
+ clanPath + "/HMMs/HMM" + familyCounts.get(index) + ".hmm",
+ false);
+
+ int count = familyCounts.get(index);
+ count++;
+ familyCounts.set(index, count);
+ }
+ line = clanFinder.readLine();
+
+ }
+ if (!inClan)
+ {
+ moveLocationBy(1, familyReader);
+ moveLocationBy(1, hmmReader);
+ }
+ filePos++;
+ // System.out.println(filePos + " files read.");
+ line = clanFinder.readLine();
+
+ }
+ clanFinder.close();
+
+ for (int clan = 0; clan < clanCount; clan++)
+ {
+ PrintWriter writer = new PrintWriter(
+ directory + "/Clan" + clan + "/NumberOfFamilies.txt");
+ int count = familyCounts.get(clan);
+ writer.print(count);
+ writer.close();
+ }
+
+ }
+
+ public String getFamilies()
+ {
+ return families;
+ }
+
+ public void setFamilies(String families)
+ {
+ this.families = currentFolder + families;
+ }
+
+ public String getHmms()
+ {
+ return hmms;
+ }
+
+ public void setHmms(String hmms)
+ {
+ this.hmms = currentFolder + hmms;
+ }
+
+ public void alignWithinClan(String exportLocation, String clansLocation)
+ throws IOException, InterruptedException
+ {
+ int alignmentsExported = 0;
+ for (int clan = 0; clan < 604; clan++)
+ {
+ System.out.println(clan);
+ int famCount = 0;
+ String clanPath = clansLocation + "/Clan" + clan;
+ int numberOfFamilies;
+ BufferedReader br = new BufferedReader(
+ new FileReader(clanPath + "/NumberOfFamilies.txt"));
+ String line = br.readLine();
+ numberOfFamilies = Integer.parseInt(line);
+ br.close();
+ if (numberOfFamilies == 1)
+ {
+ continue;
+ }
+ final String commandExportLocation = exportLocation + "/Clan" + clan;
+ createFolders(commandExportLocation);
+ for (int family = 0; family < numberOfFamilies; family++)
+ {
+ famCount++;
+ ArrayList<Integer> indexes = new ArrayList<>();
+ for (int i = 0; i < numberOfFamilies; i++)
+ {
+ if (i != family)
+ {
+ indexes.add(i);
+ }
+ }
+
+ int hmmIndex = getRandom(indexes);
+ String famPath = clanPath + "/Families/Fam" + family + ".sto";
+ String hmmPath = clanPath + "/HMMs/HMM" + hmmIndex + ".hmm";
+ String command = "/media/sf_Shared_Folder/hmmer/binaries/hmmalign --mapali "
+ + clanPath + "/Families/Fam" + hmmIndex + ".sto"
+ + " --trim ";
+ command += hmmPath + " ";
+ command += famPath;
+ final int familyIndex = family;
+ final Process p = Runtime.getRuntime().exec(command);
+
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ BufferedReader input = new BufferedReader(
+ new InputStreamReader(p.getInputStream()));
+ String line = null;
+
+ try
+ {
+ PrintWriter writer = new PrintWriter(commandExportLocation
+ + "/Families/Fam" + familyIndex + ".sto");
+ String lastLine = "";
+ boolean dataFound = false;
+ while ((line = input.readLine()) != null)
+ {
+ if (line.contains("#=GR") && !dataFound)
+ {
+ writer.println(lastLine);
+ dataFound = true;
+ }
+ if (line.contains("#") || dataFound || " ".equals(line)
+ || "".equals(line) || "//".equals(line))
+ {
+ writer.println(line);
+ }
+ lastLine = line;
+ }
+ writer.close();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }).start();
+
+ p.waitFor();
+
+ BufferedReader hmmExporter = new BufferedReader(
+ new FileReader(hmmPath));
+
+ exportFile(hmmExporter,
+ commandExportLocation + "/HMMs/HMM" + family + ".hmm",
+ false);
+
+ alignmentsExported++;
+
+
+ }
+ PrintWriter writer = new PrintWriter(
+ commandExportLocation + "/NumberOfFamilies.txt");
+ writer.print(famCount);
+ writer.close();
+ }
+
+ }
+
+ public boolean atEnd(BufferedReader br) throws IOException
+ {
+ boolean end = false;
+ br.mark(80);
+ String line = br.readLine();
+ if ("".equals(line) || line == null)
+ {
+ end = true;
+ }
+ br.reset();
+ return end;
+ }
+
+ public int getRandom(ArrayList<Integer> list)
+ {
+ if (!(list.size() > 0))
+ {
+ System.out.println("Error - size = " + list.size());
+ }
+ int index = generator.nextInt(list.size());
+ int value = list.get(index);
+ list.remove(index);
+ return value;
+ }
+
+ public void createFolders(String clanPath)
+ {
+ File clanFolder = new File(clanPath);
+ if (!clanFolder.exists())
+ {
+ clanFolder.mkdir();
+ }
+
+ File famFolder = new File(clanPath + "/Families");
+ File hmmFolder = new File(clanPath + "/HMMs");
+ if (!famFolder.exists())
+ {
+ famFolder.mkdir();
+ hmmFolder.mkdir();
+ }
+ }
+}
+
+
+
+
--- /dev/null
+package jalview.util;
+
+import java.io.IOException;
+import java.util.Scanner;
+
+/**
+ * This class contains the brain of the analyser program, and contains a number
+ * of commands for the processing of data.
+ *
+ * @author TZVanaalten
+ *
+ */
+
+public class ProbabilityAnalyserKickstarter
+{
+
+ public static void main(String[] args)
+ throws IOException, InterruptedException
+ {
+
+ // this does all of the processing
+ HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
+
+ boolean running = true;
+ System.out.println("ACTIVATED");
+ while (running)
+ {
+ Scanner keyboard = new Scanner(System.in);
+ String command = keyboard.nextLine();
+
+ Scanner inputScanner = new Scanner(command);
+ // prints family to console. Syntax is printFam <index>
+ if (command.indexOf("printFam") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ int index = inputScanner.nextInt();
+ analyser.printFam(index);
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+
+ }
+ // prints HMM to console. Syntax is printHMM <index>
+ if (command.indexOf("printHMM") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ int index = inputScanner.nextInt();
+ analyser.printHMM(index);
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ }
+ // prints family to file in current folder. Syntax is exportFam <index>.
+ if (command.indexOf("exportFam") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ int index = inputScanner.nextInt();
+ String location = inputScanner.next();
+ analyser.exportFam(index, location);
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ }
+ // prints HMM to file in current folder. Syntax is exportHMM <index>.
+ if (command.indexOf("exportHMM") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ int index = inputScanner.nextInt();
+ String location = inputScanner.next();
+ analyser.exportHMM(index, location);
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ }
+ // Processes data. Syntax is run <number of loops> <increments>. The
+ // number loops specifies the number of increments the program will run.
+ // After each increment, the data stored currently in the program is
+ // exported and re-read back into the program. This is to ensure that the
+ // program can be terminated without losing a large quantity of data. The
+ // increment is the number of families read per 'save'.
+ if (command.indexOf("run") > -1 && !(command.indexOf("ToEnd") > -1))
+ {
+ try
+ {
+
+ inputScanner.next();
+
+ int loops = inputScanner.nextInt();
+ int increments = inputScanner.nextInt();
+ boolean keepRaw = inputScanner.nextBoolean();
+
+ for (int i = 0; i < loops; i++)
+ {
+ analyser.run(increments, keepRaw);
+ System.out.println("Saved");
+ }
+ System.out.println("Task completed");
+ continue;
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ continue;
+ }
+ if ((command.indexOf("runToEnd") > -1))
+ {
+ try
+ {
+
+ inputScanner.next();
+ boolean keepRaw = inputScanner.nextBoolean();
+ boolean forClans = inputScanner.nextBoolean();
+ analyser.runToEnd(keepRaw, forClans);
+ System.out.println("Task completed");
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ continue;
+ }
+ // terminates program. Syntax is terminate.
+ if (command.indexOf("terminate") > -1)
+ {
+ running = false;
+ continue;
+ }
+ // clears files in current directory (Only a specific set of files).
+ // Syntax is clear.
+ if (command.indexOf("clear") > -1)
+ {
+ analyser.clear();
+ continue;
+ }
+ // changes current directory. Syntax is cd <directory>
+ if (command.indexOf("cd") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ analyser.setFolder(inputScanner.next());
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+
+ }
+ continue;
+ }
+
+ if (command.indexOf("getFamName") > -1)
+ {
+ try
+ {
+ inputScanner.next();
+ System.out.println(analyser.getFamilyName(inputScanner.nextInt()));
+
+ } catch (Exception e)
+ {
+ System.out.println("Command failed");
+ }
+ continue;
+ }
+ if (command.indexOf("sortIntoClans") > -1)
+ {
+ inputScanner.next();
+ analyser.sortIntoClans(inputScanner.next());
+ continue;
+
+ }
+ if (command.indexOf("setFamilies") > -1)
+ {
+ inputScanner.next();
+ analyser.setFamilies(inputScanner.next());
+ continue;
+
+ }
+
+ if (command.indexOf("setHMMs") > -1)
+ {
+ inputScanner.next();
+ analyser.setHmms(inputScanner.next());
+ continue;
+
+ }
+
+ if (command.indexOf("alignWithinClans") > -1)
+ {
+ inputScanner.next();
+ String export = inputScanner.next();
+ String clans = inputScanner.next();
+ analyser.alignWithinClan(export, clans);
+ continue;
+
+ }
+
+ System.out.println("Unrecognised command");
+ }
+
+
+
+
+ }
+
+}
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.Profiles;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
import jalview.workers.ConsensusThread;
+import jalview.workers.InformationThread;
import jalview.workers.StrucConsensusThread;
import java.awt.Color;
protected Deque<CommandI> redoList = new ArrayDeque<>();
+
/**
* alignment displayed in the viewport. Please use get/setter
*/
public boolean autoCalculateConsensus = true;
+ public boolean autoCalculateInformation = true;
+
protected boolean autoCalculateStrucConsensus = true;
protected boolean ignoreGapsInConsensusCalculation = false;
+ protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
protected ResidueShaderI residueShading = new ResidueShader();
@Override
protected AlignmentAnnotation[] groupConservation;
+ protected List<AlignmentAnnotation> groupInformation = new ArrayList<>();
+
+ protected List<AlignmentAnnotation> information = new ArrayList<>();
+
/**
* results of alignment consensus analysis for visible portion of view
*/
protected ProfilesI hconsensus = null;
/**
+ * results of information annotation analysis for the visible portion of view
+ */
+ protected List<ProfilesI> hinformation = new ArrayList<>();
+
+ /**
* results of cDNA complement consensus visible portion of view
*/
protected Hashtable[] hcomplementConsensus = null;
}
@Override
+ public void setSequenceInformationHashes(List<ProfilesI> info)
+ {
+ hinformation = info;
+ }
+
+ @Override
+ public void setSequenceInformationHash(ProfilesI info, int index)
+ {
+ hinformation.set(index, info);
+ }
+
+ @Override
+ public List<ProfilesI> getSequenceInformationHashes()
+ {
+ return hinformation;
+ }
+
+ @Override
+ public ProfilesI getSequenceInformationHash(int index)
+ {
+ return hinformation.get(index);
+ }
+
+ @Override
public Hashtable[] getComplementConsensusHash()
{
return hcomplementConsensus;
}
@Override
+ public List<AlignmentAnnotation> getInformationAnnotations()
+ {
+ return information;
+ }
+
+ @Override
+ public AlignmentAnnotation getInformationAnnotation(int index)
+ {
+ return information.get(index);
+ }
+
+ @Override
public AlignmentAnnotation getAlignmentGapAnnotation()
{
return gapcounts;
}
}
+ /**
+ * trigger update of information annotation
+ */
+ @Override
+ public void updateInformation(final AlignmentViewPanel ap)
+ {
+ if (calculator
+ .getRegisteredWorkersOfClass(InformationThread.class) == null)
+ {
+ calculator.registerWorker(new InformationThread(this, ap));
+ }
+
+ }
+
// --------START Structure Conservation
public void updateStrucConsensus(final AlignmentViewPanel ap)
{
protected boolean showConsensusHistogram = true;
/**
+ * should hmm profile be rendered by default
+ */
+ protected boolean showHMMSequenceLogo = false;
+
+ /**
+ * should hmm profile be rendered normalised to row height
+ */
+ protected boolean normaliseHMMSequenceLogo = false;
+
+ /**
+ * should information histograms be rendered by default
+ */
+ protected boolean showInformationHistogram = true;
+
+ /**
* @return the showConsensusProfile
*/
@Override
}
/**
+ * @return the showInformationProfile
+ */
+ @Override
+ public boolean isShowHMMSequenceLogo()
+ {
+ return showHMMSequenceLogo;
+ }
+
+ /**
* @param showSequenceLogo
* the new value
*/
this.showSequenceLogo = showSequenceLogo;
}
+ public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
+ {
+ if (showHMMSequenceLogo != this.showHMMSequenceLogo)
+ {
+ this.showHMMSequenceLogo = showHMMSequenceLogo;
+ calculator.updateAnnotationFor(InformationThread.class);
+ }
+ this.showHMMSequenceLogo = showHMMSequenceLogo;
+ }
+
/**
* @param showConsensusHistogram
* the showConsensusHistogram to set
}
/**
+ * @param showInformationHistogram
+ * the showInformationHistogram to set
+ */
+ public void setShowInformationHistogram(boolean showInformationHistogram)
+ {
+ this.showInformationHistogram = showInformationHistogram;
+ }
+
+ /**
* @return the showGroupConservation
*/
public boolean isShowGroupConservation()
}
/**
+ *
+ * @return flag to indicate if the information content histogram should be
+ * rendered by default
+ */
+ @Override
+ public boolean isShowInformationHistogram()
+ {
+ return this.showInformationHistogram;
+ }
+
+ /**
* when set, updateAlignment will always ensure sequences are of equal length
*/
private boolean padGaps = false;
}
+ public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
+ {
+ ignoreBelowBackGroundFrequencyCalculation = b;
+ if (ap != null)
+ {
+ updateInformation(ap);
+ }
+
+ }
+
private long sgrouphash = -1, colselhash = -1;
/**
return ignoreGapsInConsensusCalculation;
}
+ @Override
+ public boolean isIgnoreBelowBackground()
+ {
+ return ignoreBelowBackGroundFrequencyCalculation;
+ }
+
// property change stuff
// JBPNote Prolly only need this in the applet version.
private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
{
updateStrucConsensus(ap);
}
+ updateInformation(ap);
+
+ List<SequenceI> hmmSequences;
+ hmmSequences = alignment.getHMMConsensusSequences(false);
+
+ for (SequenceI seq : hmmSequences)
+ {
+ seq.updateHMMMapping();
+ }
// Reset endRes of groups if beyond alignment width
int alWidth = alignment.getWidth();
MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
+
initGapCounts();
initComplementConsensus();
}
}
+ @Override
+ public void initInformation()
+ {
+ for (SequenceI seq : alignment.getHMMConsensusSequences(false))
+ {
+ if (!seq.hasHMMAnnotation())
+ {
+ AlignmentAnnotation information;
+ information = new AlignmentAnnotation(seq.getName(),
+ MessageManager.getString("label.information_description"),
+ new Annotation[1], 0f, 6.52f,
+ AlignmentAnnotation.BAR_GRAPH);
+ information.hasText = true;
+ information.autoCalculated = true;
+ information.hasText = true;
+ information.autoCalculated = false;
+ information.sequenceRef = seq;
+ information.setCalcId("HMM annotation");
+ this.information.add(information);
+ hinformation.add(new Profiles(new ProfileI[1]));
+ alignment.addAnnotation(information);
+ seq.updateHMMMapping();
+ seq.setHasInfo(true);
+ seq.addAlignmentAnnotation(information);
+ }
+ }
+
+ }
+
// these should be extracted from the view model - style and settings for
// derived annotation
private void initGapCounts()
boolean showprf = isShowSequenceLogo();
boolean showConsHist = isShowConsensusHistogram();
boolean normLogo = isNormaliseSequenceLogo();
+ boolean showHMMPrf = isShowHMMSequenceLogo();
+ boolean showInfoHist = isShowInformationHistogram();
+ boolean normHMMLogo = isNormaliseHMMSequenceLogo();
/**
* TODO reorder the annotation rows according to group/sequence ordering on
sg.setshowSequenceLogo(showprf);
sg.setShowConsensusHistogram(showConsHist);
sg.setNormaliseSequenceLogo(normLogo);
+ sg.setshowHMMSequenceLogo(showHMMPrf);
+ sg.setShowInformationHistogram(showInfoHist);
+ sg.setNormaliseHMMSequenceLogo(normHMMLogo);
}
if (conv)
{
.synchronizedList(new ArrayList<AlignCalcWorkerI>());
updating = Collections.synchronizedMap(
new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
- canUpdate = new HashSet<AlignCalcWorkerI>();
+ canUpdate = new HashSet<>();
}
@Override
public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
Class<? extends AlignCalcWorkerI> workerClass)
{
- List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
+ List<AlignCalcWorkerI> workingClass = new ArrayList<>();
synchronized (canUpdate)
{
for (AlignCalcWorkerI worker : canUpdate)
public void removeRegisteredWorkersOfClass(
Class<? extends AlignCalcWorkerI> typeToRemove)
{
- List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
- Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
+ List<AlignCalcWorkerI> removable = new ArrayList<>();
+ Set<AlignCalcWorkerI> toremovannot = new HashSet<>();
synchronized (restartable)
{
for (AlignCalcWorkerI worker : restartable)
* first just find those to remove (to avoid
* ConcurrentModificationException)
*/
- List<AlignCalcWorkerI> toRemove = new ArrayList<AlignCalcWorkerI>();
+ List<AlignCalcWorkerI> toRemove = new ArrayList<>();
for (AlignCalcWorkerI worker : restartable)
{
if (worker.involves(ann))
--- /dev/null
+package jalview.workers;
+
+import jalview.analysis.AAFrequency;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
+
+import java.util.List;
+
+public class InformationThread extends AlignCalcWorker
+{
+ /**
+ * Constructor for information thread.
+ *
+ * @param alignViewport
+ * @param alignPanel
+ */
+ public InformationThread(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ @Override
+ public void run()
+ {
+ if (calcMan.isPending(this))
+ {
+ return;
+ }
+ calcMan.notifyStart(this);
+ long started = System.currentTimeMillis();
+
+ List<AlignmentAnnotation> information = getInformationAnnotations();
+ try
+ {
+ if ((information == null) || calcMan.isPending(this))
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+ while (!calcMan.notifyWorking(this))
+ {
+ // System.err.println("Thread
+ // (Information"+Thread.currentThread().getName()+") Waiting around.");
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ if (alignViewport.isClosed())
+ {
+ abortAndDestroy();
+ return;
+ }
+ AlignmentI alignment = alignViewport.getAlignment();
+
+ int aWidth = -1;
+
+ if (alignment == null || (aWidth = alignment.getWidth()) < 0)
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+
+ eraseInformation(aWidth);
+ computeInformation(alignment);
+ updateResultAnnotation(true);
+
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
+ } catch (OutOfMemoryError error)
+ {
+ calcMan.disableWorker(this);
+ ap.raiseOOMWarning("calculating information", error);
+ } finally
+ {
+ calcMan.workerComplete(this);
+ }
+
+
+
+ }
+
+ /**
+ * Clear out any existing information annotations
+ *
+ * @param aWidth
+ * the width (number of columns) of the annotated alignment
+ */
+ protected void eraseInformation(int aWidth)
+ {
+
+ List<AlignmentAnnotation> information = getInformationAnnotations();
+ for (AlignmentAnnotation info : information)
+ {
+ info.annotations = new Annotation[aWidth];
+ }
+ }
+
+
+ /**
+ * Computes the profiles from a HMM for an alignment.
+ *
+ * @param alignment
+ */
+ protected void computeInformation(AlignmentI alignment)
+ {
+
+ int width = alignment.getWidth();
+ List<SequenceI> hmmSeqs = alignment.getHMMConsensusSequences(false);
+ int index = 0;
+ for (SequenceI seq : hmmSeqs)
+ {
+ HiddenMarkovModel hmm = seq.getHMM();
+ ProfilesI hinformation = AAFrequency.calculateHMMProfiles(hmm, width,
+ 0, width, true, alignViewport.isIgnoreBelowBackground());
+ alignViewport.setSequenceInformationHash(hinformation, index);
+ // setColourSchemeInformation(hinformation);
+ index++;
+ }
+ }
+
+ /**
+ * gets the sequences on the alignment on the viewport.
+ *
+ * @return
+ */
+ protected SequenceI[] getSequences()
+ {
+ return alignViewport.getAlignment().getSequencesArray();
+ }
+
+ protected void setColourSchemeInformation(ProfilesI information)
+ {
+ ResidueShaderI cs = alignViewport.getResidueShading();
+ if (cs != null)
+ {
+ cs.setInformation(information);
+ }
+ }
+
+ /**
+ * Get the Information annotation for the alignment
+ *
+ * @return
+ */
+ protected List<AlignmentAnnotation> getInformationAnnotations()
+ {
+ return alignViewport.getInformationAnnotations();
+ }
+
+ /**
+ * Get the Gap annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getGapAnnotation()
+ {
+ return alignViewport.getAlignmentGapAnnotation();
+ }
+
+ /**
+ * update the information annotation from the sequence profile data using
+ * current visualization settings.
+ */
+ @Override
+ public void updateAnnotation()
+ {
+
+ updateResultAnnotation(false);
+ }
+
+ /**
+ * Derives the information content for an information annotation.
+ *
+ * @param immediate
+ */
+ public void updateResultAnnotation(boolean immediate)
+ {
+ List<AlignmentAnnotation> annots = getInformationAnnotations();
+ int index = 0;
+ for (AlignmentAnnotation information : annots)
+ {
+ ProfilesI hinformation = (ProfilesI) getSequenceInformation(index);
+ if (immediate || !calcMan.isWorking(this) && information != null
+ && hinformation != null)
+ {
+ deriveInformation(information, hinformation);
+ }
+ index++;
+ }
+ }
+
+ /**
+ * Convert the computed information data into the desired annotation for
+ * display.
+ *
+ * @param informationAnnotation
+ * the annotation to be populated
+ * @param hinformation
+ * the computed information data
+ */
+ protected void deriveInformation(
+ AlignmentAnnotation informationAnnotation, ProfilesI hinformation)
+ {
+
+ long nseq = getSequences().length;
+ AAFrequency.completeInformation(informationAnnotation, hinformation,
+ hinformation.getStartColumn(), hinformation.getEndColumn() + 1,
+ alignViewport.isIgnoreBelowBackground(),
+ alignViewport.isShowHMMSequenceLogo(), nseq);
+ }
+
+
+
+ /**
+ * Get the information data stored on the viewport.
+ *
+ * @return
+ */
+ protected Object getSequenceInformation(int index)
+ {
+ // TODO convert ComplementInformationThread to use Profile
+ return alignViewport.getSequenceInformationHash(index);
+ }
+ }
+
+
+
+
+
/**
* input
*/
- ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
+ ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
/**
* output
compbio.data.sequence.FastaSequence seq;
for (int i = 0, n = 0; i < seqs.length; i++)
{
-
String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
// for
// any
public List<Argument> getJabaArguments()
{
- List<Argument> newargs = new ArrayList<Argument>();
+ List<Argument> newargs = new ArrayList<>();
if (preset != null && preset instanceof JabaWsParamSet)
{
newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
void displayResults(boolean newFrame)
{
// view input or result data for each block
- List<AlignmentOrder> alorders = new ArrayList<AlignmentOrder>();
+ List<AlignmentOrder> alorders = new ArrayList<>();
SequenceI[][] results = new SequenceI[jobs.length][];
AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
String lastProgram = null;
if (newFrame)
{
displayInNewFrame(al, alorders, hidden);
-
}
else
{
else
{
// construct a non-redundant ordering set
- List<String> names = new ArrayList<String>();
+ List<String> names = new ArrayList<>();
for (int i = 0, l = alorders.size(); i < l; i++)
{
String orderName = " Region " + i;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.Profile;
import jalview.datamodel.ProfileI;
+import jalview.datamodel.Profiles;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AAFrequencyTest
{
+ HiddenMarkovModel hmm;
+
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
assertEquals("T 75%", ann.description);
assertEquals("T", ann.displayCharacter);
}
+
+
+ @Test(groups = { "Functional" }, priority = 1)
+ public void testExtractHMMProfile()
+ throws MalformedURLException, IOException
+ {
+
+ HMMFile hmmFile = new HMMFile(new FileParse(
+ "test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE));
+ hmm = hmmFile.getHMM();
+ int[] expected = { 0, 4, 100, 'T', 71, 'C', 12, 'G', 9, 'A', 9 };
+ int[] actual = AAFrequency.extractHMMProfile(hmm, 17, false);
+ for (int i = 0; i < actual.length; i++)
+ {
+ if (i == 2)
+ {
+ assertEquals(actual[i], expected[i]);
+ }
+ else
+ {
+ assertEquals(actual[i], expected[i]);
+ }
+ }
+
+ int[] expected2 = { 0, 4, 100, 'A', 85, 'C', 0, 'G', 0, 'T', 0 };
+ int[] actual2 = AAFrequency.extractHMMProfile(hmm, 2, true);
+ for (int i = 0; i < actual2.length; i++)
+ {
+ if (i == 2)
+ {
+ assertEquals(actual[i], expected[i]);
+ }
+ else
+ {
+ assertEquals(actual[i], expected[i]);
+ }
+ }
+
+ assertNull(AAFrequency.extractHMMProfile(null, 98978867, true));
+ }
+
+ @Test(groups = { "Functional" }, priority = 2)
+ public void testGetAnalogueCount()
+ {
+ int count;
+ count = AAFrequency.getAnalogueCount(hmm, 0, 'T', false);
+ assertEquals(7859, count);
+ count = AAFrequency.getAnalogueCount(hmm, 20, 'G', false);
+ assertEquals(7546, count);
+ count = AAFrequency.getAnalogueCount(hmm, 1077, 'G', true);
+ assertEquals(0, count);
+ }
+
+ @Test(groups = { "Functional" }, priority = 3)
+ public void testCompleteInformation()
+ {
+ ProfileI prof1 = new Profile(1, 0, 100, "A");
+ ProfileI prof2 = new Profile(1, 0, 100, "-");
+
+ ProfilesI profs = new Profiles(new ProfileI[] { prof1, prof2 });
+ Annotation ann1 = new Annotation(6.5f);
+ Annotation ann2 = new Annotation(0f);
+ Annotation[] annots = new Annotation[] { ann1, ann2 };
+ SequenceI seq = new Sequence("", "AA", 0, 0);
+ seq.setHMM(hmm);
+ AlignmentAnnotation annot = new AlignmentAnnotation("", "", annots);
+ annot.setSequenceRef(seq);
+ AAFrequency.completeInformation(annot, profs, 0, 1, false, true, 1);
+ float ic = annot.annotations[0].value;
+ assertEquals(0.91532f, ic, 0.0001f);
+ ic = annot.annotations[1].value;
+ assertEquals(0f, ic, 0.0001f);
+ int i = 0;
+ }
+
}
--- /dev/null
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.Test;
+
+public class HiddenMarkovModelTest {
+
+ HiddenMarkovModel hmm;
+
+ @Test(priority = 0)
+ public void testGetMatchEmissionProbabilities()
+ throws MalformedURLException, IOException
+ {
+ HMMFile file = new HMMFile(new FileParse(
+ "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
+ hmm = file.getHMM();
+
+ double[] actual = new double[4];
+ actual[0] = hmm.getMatchEmissionProbability(0, 'R');
+ actual[1] = hmm.getMatchEmissionProbability(19, 'W');
+ actual[2] = hmm.getMatchEmissionProbability(160, 'G');
+ actual[3] = hmm.getMatchEmissionProbability(475, 'A');
+
+ double[] expected = new double[4];
+ expected[0] = 0.02537400637;
+ expected[1] = 0.00588228492;
+ expected[2] = 0;
+ expected[3] = 0.04995163708;
+
+ for (int i = 0; i < 4; i++)
+ {
+ assertEquals(actual[i], expected[i], 0.001d);
+ }
+ }
+
+ @Test(priority = 1)
+ public void testGetInsertEmissionProbabilities()
+ {
+ double[] actual = new double[4];
+ actual[0] = hmm.getInsertEmissionProbability(2, 'A');
+ actual[1] = hmm.getInsertEmissionProbability(5, 'T');
+ actual[2] = hmm.getInsertEmissionProbability(161, 'K');
+ actual[3] = hmm.getInsertEmissionProbability(472, 'L');
+
+ double[] expected = new double[4];
+ expected[0] = 0.06841384927;
+ expected[1] = 0.06233763141;
+ expected[2] = 0;
+ expected[3] = 0.06764038926;
+
+ for (int i = 0; i < 4; i++)
+ {
+ assertEquals(actual[i], expected[i], 0.001d);
+ }
+ }
+
+ @Test(priority = 1)
+ public void testGetStateTransitionProbabilities()
+ {
+ double[] actual = new double[4];
+ actual[0] = hmm.getStateTransitionProbability(475, hmm.MATCHTODELETE);
+ actual[1] = hmm.getStateTransitionProbability(8, hmm.MATCHTOINSERT);
+ actual[2] = hmm.getStateTransitionProbability(80, hmm.INSERTTOINSERT);
+ actual[3] = hmm.getStateTransitionProbability(475, hmm.DELETETOMATCH);
+
+ double[] expected = new double[4];
+ expected[0] = Double.NEGATIVE_INFINITY;
+ expected[1] = 0.00662894243;
+ expected[2] = 0.46183388908;
+ expected[3] = 1;
+
+ for (int i = 0; i < 4; i++)
+ {
+ assertEquals(actual[i], expected[i], 0.001d);
+ }
+ }
+
+ @Test(priority = 1)
+ public void testGetConsensusAtAlignColumn()
+ {
+ char[] cons = new char[4];
+ cons[0] = hmm.getConsensusAtAlignColumn(10);
+ cons[1] = hmm.getConsensusAtAlignColumn(50);
+ hmm.setConsensusResidueStatus(false);
+ cons[2] = hmm.getConsensusAtAlignColumn(100);
+ cons[3] = hmm.getConsensusAtAlignColumn(400);
+
+ char[] expected = new char[4];
+ expected[0] = 's';
+ expected[1] = 'k';
+ expected[2] = 'l';
+ expected[3] = 'k';
+
+ for (int i = 0; i < 4; i++)
+ {
+ assertEquals(cons[i], expected[i]);
+ }
+
+ }
+
+ @Test(priority = 1)
+ public void testGetConsensusSequence()
+ {
+ SequenceI seq = hmm.getConsensusSequence();
+ String subStr = seq.getSequenceAsString().substring(0, 10);
+ assertEquals(subStr, "YELLEKLGSG");
+ subStr = seq.getSequenceAsString().substring(150, 161);
+ assertEquals(subStr, "-DLLK------");
+ }
+}
--- /dev/null
+package jalview.hmmer;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotEquals;
+import static org.testng.Assert.fail;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.DataSourceType;
+import jalview.io.FastaFile;
+import jalview.io.FileParse;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+
+public class HMMERTest {
+
+ AlignFrame frame;
+
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ Jalview.main(
+ new String[]
+ { "-noquestionnaire", "-nonews", "-props",
+ "test/jalview/hmmer/testProps.jvprops" });
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(priority = 0)
+ public void testHMMBuild() throws MalformedURLException, IOException
+ {
+ FastaFile file = null;
+ try
+ {
+ file = new FastaFile(
+ new FileParse("examples/uniref50.fa", DataSourceType.FILE));
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ fail();
+ }
+ SequenceI[] seqs = file.getSeqsAsArray();
+ AlignmentI al = new Alignment(seqs);
+ frame = new AlignFrame(al, 150, 20);
+
+ HMMBuildThread thread = new HMMBuildThread(frame);
+ thread.hmmbuildWaitTillComplete();
+
+ SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
+ HiddenMarkovModel hmm = seq.getHMM();
+ if (hmm == null)
+ {
+ fail();
+ }
+
+ assertEquals(hmm.getLength().intValue(), 148);
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertEquals(hmm.getName(), "Alignment");
+ assertEquals(hmm.getEffectiveNumberOfSequences(), 0.648193, 0.0001);
+ assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
+ }
+
+ @Test(priority = 1)
+ public void testHMMAlign() throws MalformedURLException, IOException
+ {
+ HMMAlignThread thread = new HMMAlignThread(frame, true);
+ try
+ {
+ thread.hmmalignWaitTillComplete();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ fail();
+ }
+
+ if (Desktop.getAlignFrames() == null)
+ {
+ fail();
+ }
+
+ AlignFrame frame = Desktop.getAlignFrames()[0];
+ AlignmentI al = frame.getViewport().getAlignment();
+ assertNotEquals(al, null);
+ List<SequenceI> hmmSeqs = al.getHMMConsensusSequences(false);
+ assertNotEquals(hmmSeqs, null);
+
+ }
+}
+
@Test(groups = "Functional")
public void testGetReadableFormats()
{
- String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getReadableFormats().toString(), expected);
}
@Test(groups = "Functional")
public void testGetWritableFormats()
{
- String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
+ String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getWritableFormats(true).toString(), expected);
- expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview]";
+ expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview, HMMER3]";
assertEquals(formats.getWritableFormats(false).toString(), expected);
}
@Test(groups = "Functional")
public void testDeregisterFileFormat()
{
- String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+ String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
FileFormats formats = FileFormats.getInstance();
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
formats.deregisterFileFormat(FileFormat.Fasta.getName());
- writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+ writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
* re-register the format: it gets added to the end of the list
*/
formats.registerFileFormat(FileFormat.Fasta);
- writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
- readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
+ writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3, Fasta]";
+ readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, Fasta]";
assertEquals(formats.getWritableFormats(true).toString(), writable);
assertEquals(formats.getReadableFormats().toString(), readable);
}
{
try
{
- AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+ AlignmentI al;
+ if (format == FileFormat.HMMER3)
+ {
+ al = new FormatAdapter().readFile("examples/uniref50_hmm.hmm",
+ DataSourceType.FILE, FileFormat.HMMER3);
+ }
+ else
+ {
+ al = new FormatAdapter().readFile("examples/uniref50.fa",
DataSourceType.FILE, FileFormat.Fasta);
+ }
/*
* 'gap' is the gap character used in the alignment data file here,
AlignmentI reloaded = new FormatAdapter().readFile(formatted,
DataSourceType.PASTE, format);
List<SequenceI> reread = reloaded.getSequences();
- assertEquals("Wrong number of reloaded sequences", seqs.length,
- reread.size());
+ assertEquals("Wrong number of reloaded sequences", seqs.length,
+ reread.size());
+
int i = 0;
for (SequenceI seq : reread)
@DataProvider(name = "formats")
static Object[][] getFormats()
{
- List<FileFormatI> both = new ArrayList<FileFormatI>();
+ List<FileFormatI> both = new ArrayList<>();
for (FileFormatI format : FileFormats.getInstance().getFormats())
{
if (format.isReadable() && format.isWritable()
--- /dev/null
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+import org.testng.annotations.Test;
+
+public class HMMFileTest {
+
+
+
+ HMMFile fn3 = new HMMFile(new BufferedReader(
+ new FileReader(("test/jalview/io/test_fn3_hmm.txt"))));
+
+ HMMFile pKinase = new HMMFile(new BufferedReader(
+ new FileReader(("test/jalview/io/test_PKinase_hmm.txt"))));
+
+ HMMFile made1 = new HMMFile(new BufferedReader(
+ new FileReader(("test/jalview/io/test_MADE1_hmm.txt"))));
+
+ HMMFileTest() throws IOException
+ {
+
+ }
+
+
+
+
+ @Test
+ public void testParse() throws IOException
+ {
+
+ pKinase.parse();
+ HiddenMarkovModel hmm = pKinase.getHMM();
+ assertEquals(hmm.getName(), "Pkinase");
+ assertEquals(hmm.getAccessionNumber(), "PF00069.17");
+ assertEquals(hmm.getDescription(), "Protein kinase domain");
+ assertEquals(hmm.getLength().intValue(), 260);
+ assertNull(hmm.getMaxInstanceLength());
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertEquals(hmm.referenceAnnotationIsActive(), false);
+ assertEquals(hmm.maskValueIsActive(), false);
+ assertEquals(hmm.consensusResidueIsActive(), true);
+ assertEquals(hmm.consensusStructureIsActive(),
+ true);
+ assertEquals(hmm.mapIsActive(), true);
+ assertEquals(hmm.getDate(), "Thu Jun 16 11:44:06 2011");
+ assertNull(hmm.getCommandLineLog());
+ assertEquals(hmm.getNumberOfSequences().intValue(), 54);
+ assertEquals(hmm.getEffectiveNumberOfSequences(), 3.358521, 4d);
+ assertEquals(hmm.getCheckSum().longValue(), 3106786190l);
+ assertEquals(hmm.getGatheringThreshold(), "70.30 70.30");
+ assertEquals(hmm.getTrustedCutoff(), "70.30 70.30");
+ assertEquals(hmm.getNoiseCutoff(), "70.20 70.20");
+
+ List<Character> symbols = new ArrayList<>();
+ symbols.add('A');
+ symbols.add('C');
+ symbols.add('D');
+ symbols.add('E');
+ symbols.add('F');
+ symbols.add('G');
+ symbols.add('H');
+ symbols.add('I');
+ symbols.add('K');
+ symbols.add('L');
+ symbols.add('M');
+ symbols.add('N');
+ symbols.add('P');
+ symbols.add('Q');
+ symbols.add('R');
+ symbols.add('S');
+ symbols.add('T');
+ symbols.add('V');
+ symbols.add('W');
+ symbols.add('Y');
+
+ assertEquals(hmm.getSymbols(), symbols);
+
+ assertEquals(hmm.getMatchEmissionProbability(0, 'Y'), 0.16102, 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(11, 'P'), 0.0130, 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(24, 'I'), 0.02583, 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(83, 'C'), 0.008549,
+ 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(332, 'E'), 0.07998,
+ 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(381, 'D'), 0.014465,
+ 0.001d);
+ assertEquals(hmm.getMatchEmissionProbability(475, 'Y'), 0.02213,
+ 0.001d);
+
+ assertEquals(hmm.getInsertEmissionProbability(1, 'C'), 0.012, 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(14, 'H'), 0.02411,
+ 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(23, 'L'), 0.06764,
+ 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(90, 'D'), 0.0623, 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(374, 'T'), 0.0623,
+ 0.001d);
+ assertEquals(hmm.getInsertEmissionProbability(470, 'P'), 0.0647,
+ 0.001d);
+
+ assertEquals(hmm.getStateTransitionProbability(2, 6), 0.3848, 0.001d);
+ assertEquals(hmm.getStateTransitionProbability(38, 3), 0.5382, 0.001d);
+ assertEquals(hmm.getStateTransitionProbability(305, 3), 0.2916, 0.001d);
+ assertEquals(hmm.getStateTransitionProbability(380, 0), 0.99, 0.001d);
+ assertEquals(hmm.getStateTransitionProbability(453, 1), 0.0066, 0.001d);
+
+ assertEquals(hmm.getNodeAlignmentColumn(3).intValue(), 2);
+ assertEquals(hmm.getReferenceAnnotation(7), '-');
+ assertEquals(hmm.getConsensusResidue(23), 't');
+ assertEquals(hmm.getMaskedValue(30), '-');
+ assertEquals(hmm.getConsensusStructure(56), 'S');
+
+ assertEquals(hmm.getNodeAlignmentColumn(78).intValue(), 135);
+ assertEquals(hmm.getReferenceAnnotation(93), '-');
+ assertEquals(hmm.getConsensusResidue(145), 'a');
+ assertEquals(hmm.getMaskedValue(183), '-');
+ assertEquals(hmm.getConsensusStructure(240), 'H');
+
+ }
+
+ @Test(priority = 0)
+ public void testParseFileProperties() throws IOException
+ {
+ FileReader fr = new FileReader(
+ new File("test/jalview/io/test_fn3_hmm.txt"));
+ BufferedReader br = new BufferedReader(fr);
+ fn3.setHMM(new HiddenMarkovModel());
+ fn3.parseFileProperties(br);
+ fn3.parseModel(br); // this is for a later test
+ HiddenMarkovModel testHMM = new HiddenMarkovModel();
+ testHMM = fn3.getHMM();
+ br.close();
+ fr.close();
+
+ assertEquals(testHMM.getName(), "fn3");
+ assertEquals(testHMM.getAccessionNumber(), "PF00041.13");
+ assertEquals(testHMM.getDescription(),
+ "Fibronectin type III domain");
+ assertEquals(testHMM.getLength().intValue(), 86);
+ assertNull(testHMM.getMaxInstanceLength());
+ assertEquals(testHMM.getAlphabetType(), "amino");
+ assertEquals(testHMM.referenceAnnotationIsActive(), false);
+ assertEquals(testHMM.maskValueIsActive(), false);
+ assertEquals(testHMM.consensusResidueIsActive(), true);
+ assertEquals(testHMM.consensusStructureIsActive(), true);
+ assertEquals(testHMM.mapIsActive(), true);
+ assertEquals(testHMM.getDate(), "Fri Jun 20 08:22:31 2014");
+ assertNull(testHMM.getCommandLineLog());
+ assertEquals(testHMM.getNumberOfSequences().intValue(), 106);
+ assertEquals(testHMM.getEffectiveNumberOfSequences(), 11.415833, 4d);
+ assertEquals(testHMM.getCheckSum().longValue(), 3564431818l);
+ assertEquals(testHMM.getGatheringThreshold(), "8.00 7.20");
+ assertEquals(testHMM.getTrustedCutoff(), "8.00 7.20");
+ assertEquals(testHMM.getNoiseCutoff(), "7.90 7.90");
+ assertEquals(testHMM.getViterbi(), "-9.7737 0.71847");
+ assertEquals(testHMM.getMSV(), "-9.4043 0.71847");
+ assertEquals(testHMM.getForward(), "-3.8341 0.71847");
+
+
+ FileReader fr3 = new FileReader(
+ new File("test/jalview/io/test_MADE1_hmm.txt"));
+ BufferedReader br3 = new BufferedReader(fr3);
+ made1.setHMM(new HiddenMarkovModel());
+ made1.parseFileProperties(br3);
+ testHMM = made1.getHMM();
+ br3.close();
+ fr3.close();
+
+ assertEquals(testHMM.getName(), "MADE1");
+ assertEquals(testHMM.getAccessionNumber(), "DF0000629.2");
+ assertEquals(testHMM.getDescription(),
+ "MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon");
+ assertEquals(testHMM.getLength().intValue(), 80);
+ assertEquals(testHMM.getMaxInstanceLength().intValue(), 426);
+ assertEquals(testHMM.getAlphabetType(), "DNA");
+ assertEquals(testHMM.referenceAnnotationIsActive(), true);
+ assertEquals(testHMM.maskValueIsActive(), false);
+ assertEquals(testHMM.consensusResidueIsActive(), true);
+ assertEquals(testHMM.consensusStructureIsActive(), false);
+ assertEquals(testHMM.mapIsActive(), true);
+ assertEquals(testHMM.getDate(), "Tue Feb 19 20:33:41 2013");
+ assertNull(testHMM.getCommandLineLog());
+ assertEquals(testHMM.getNumberOfSequences().intValue(), 1997);
+ assertEquals(testHMM.getEffectiveNumberOfSequences(), 3.911818, 4d);
+ assertEquals(testHMM.getCheckSum().longValue(), 3015610723l);
+ assertEquals(testHMM.getGatheringThreshold(), "2.324 4.234");
+ assertEquals(testHMM.getTrustedCutoff(), "2.343 1.212");
+ assertEquals(testHMM.getNoiseCutoff(), "2.354 5.456");
+ assertEquals(testHMM.getViterbi(), "-9.3632 0.71858");
+ assertEquals(testHMM.getMSV(), "-8.5786 0.71858");
+ assertEquals(testHMM.getForward(), "-3.4823 0.71858");
+
+
+ }
+
+ @Test
+ public void testFillList() throws IOException
+ {
+ Scanner scanner1 = new Scanner("1.3 2.4 5.3 3.9 9.8 4.7 4.3 2.3 6.9");
+ ArrayList<Double> filledArray = new ArrayList<>();
+
+ filledArray.add(0.27253);
+ filledArray.add(0.0907);
+ filledArray.add(0.00499);
+ filledArray.add(0.02024);
+ filledArray.add(0.00005);
+ filledArray.add(0.00909);
+ filledArray.add(0.01357);
+ filledArray.add(0.10026);
+ filledArray.add(0.001);
+
+ List<Double> testList = HMMFile.fillList(scanner1, 9);
+
+ for (int i = 0; i < 9; i++)
+ {
+ assertEquals(testList.get(i), filledArray.get(i), 0.001d);
+
+ }
+
+ filledArray.clear();
+ scanner1.close();
+
+ Scanner scanner2 = new Scanner(
+ "1.346 5.554 35.345 5.64 1.4");
+ filledArray.add(0.2603);
+ filledArray.add(0.00387);
+ filledArray.add(0d);
+ filledArray.add(0.00355);
+ filledArray.add(0.2466);
+
+ testList = HMMFile.fillList(scanner2, 5);
+
+ for (int i = 0; i < 5; i++)
+ {
+ assertEquals(testList.get(i), filledArray.get(i), 0.001d);
+ }
+
+ }
+
+ @Test
+ public void testParseModel() throws IOException
+ {
+ FileReader fr = new FileReader(
+ new File("test/jalview/io/test_MADE1_hmm.txt"));
+ BufferedReader br = new BufferedReader(fr);
+ HiddenMarkovModel testHMM = new HiddenMarkovModel();
+ for (int i = 0; i < 24; i++)
+ {
+ br.readLine();
+ }
+
+ made1.parseModel(br);
+ testHMM = made1.getHMM();
+
+ br.close();
+ fr.close();
+
+ assertEquals(testHMM.getMatchEmissionProbability(1, 'C'), 0.09267,
+ 0.001d);
+ assertEquals(testHMM.getMatchEmissionProbability(25, 'G'), 0.07327,
+ 0.001d);
+ assertEquals(testHMM.getMatchEmissionProbability(1092, 'C'), 0.04184,
+ 0.001d);
+ assertEquals(testHMM.getMatchEmissionProbability(1107, 'G'), 0.07,
+ 0.001d);
+
+ assertEquals(testHMM.getInsertEmissionProbability(0, 'G'), 0.25,
+ 0.001d);
+ assertEquals(testHMM.getInsertEmissionProbability(247, 'T'), 0.2776,
+ 0.001d);
+ assertEquals(testHMM.getInsertEmissionProbability(1096, 'T'), 0.25,
+ 0.001d);
+ assertEquals(testHMM.getInsertEmissionProbability(1111, 'T'), 0.25,
+ 0.001d);
+
+ assertEquals(testHMM.getStateTransitionProbability(1, 0), 0.9634,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(5, 1), 0.0203,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(14, 3), 0.2515,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(65, 4), 0.78808,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(1080, 2), 0.01845,
+ 0.001d);
+ assertEquals(testHMM.getStateTransitionProbability(1111, 6),
+ Double.NEGATIVE_INFINITY);
+
+ }
+
+ @Test
+ public void testParseAnnotations()
+ {
+ HMMFile testFile = new HMMFile();
+ testFile.setHMM(new HiddenMarkovModel());
+ testFile.getHMM().getNodes().add(new HMMNode());
+ testFile.getHMM().getNodes().add(new HMMNode());
+ testFile.getHMM().getNodes().add(new HMMNode());
+
+
+ testFile.getHMM().setConsensusResidueStatus(true);
+ testFile.getHMM().setMAPStatus(true);
+ testFile.getHMM().setReferenceAnnotationStatus(true);
+ testFile.getHMM().setConsensusStructureStatus(true);
+ testFile.getHMM().setMaskedValueStatus(true);
+ Scanner scanner = new Scanner("1345 t t t t");
+ testFile.parseAnnotations(scanner, 1);
+
+ testFile.getHMM().setConsensusResidueStatus(true);
+ testFile.getHMM().setMAPStatus(false);
+ testFile.getHMM().setReferenceAnnotationStatus(true);
+ testFile.getHMM().setConsensusStructureStatus(false);
+ testFile.getHMM().setMaskedValueStatus(false);
+ Scanner scanner2 = new Scanner("- y x - -");
+ testFile.parseAnnotations(scanner2, 2);
+
+ HiddenMarkovModel hmm = testFile.getHMM();
+
+ assertEquals(hmm.getNodeAlignmentColumn(1).intValue(), 1344);
+ assertEquals(hmm.getConsensusResidue(1), 't');
+ assertEquals(hmm.getReferenceAnnotation(1), 't');
+ assertEquals(hmm.getMaskedValue(1), 't');
+ assertEquals(hmm.getConsensusStructure(1), 't');
+
+ assertEquals(hmm.findNodeIndex(1344).intValue(), 1);
+
+ scanner.close();
+
+ }
+
+ /**
+ * tests to see if file produced by the output matches the file from the input
+ *
+ * @throws IOException
+ */
+
+
+ @Test(priority = 3)
+ public void testPrint() throws IOException
+ {
+ PrintWriter writer = new PrintWriter(
+ "test/jalview/io/test_export_hmm.txt");
+ String output = pKinase.print();
+ writer.print(output);
+ writer.close();
+ HMMFile pKinaseClone = new HMMFile(
+ new FileParse("test/jalview/io/test_export_hmm.txt",
+ DataSourceType.FILE));
+ HiddenMarkovModel pKinaseHMM = new HiddenMarkovModel();
+ HiddenMarkovModel pKinaseCloneHMM = new HiddenMarkovModel();
+ pKinaseHMM = pKinase.getHMM();
+ pKinaseCloneHMM = pKinaseClone.getHMM();
+
+ for (int i = 0; i < pKinaseHMM.getLength(); i++)
+ {
+ List<Double> list1;
+ List<Double> list2;
+ boolean result;
+
+ list1 = pKinaseHMM.getNode(i).getMatchEmissions();
+ list2 = pKinaseCloneHMM.getNode(i).getMatchEmissions();
+
+ result = checkIfListsAreIdentical(list1, list2);
+ assertEquals(result, true);
+
+ list1 = pKinaseHMM.getNode(i).getInsertEmissions();
+ list2 = pKinaseCloneHMM.getNode(i).getInsertEmissions();
+
+ result = checkIfListsAreIdentical(list1, list2);
+ assertEquals(result, true);
+
+ list1 = pKinaseHMM.getNode(i).getStateTransitions();
+ list2 = pKinaseCloneHMM.getNode(i).getStateTransitions();
+
+ result = checkIfListsAreIdentical(list1, list2);
+ assertEquals(result, true);
+
+ if (i > 0)
+ {
+ int alignColumn1;
+ int alignColumn2;
+
+ alignColumn1 = pKinaseHMM.getNodeAlignmentColumn(i);
+ alignColumn2 = pKinaseCloneHMM.getNodeAlignmentColumn(i);
+
+ assertEquals(alignColumn1, alignColumn2);
+
+ char annotation1;
+ char annotation2;
+
+ annotation1 = pKinaseHMM.getReferenceAnnotation(i);
+ annotation2 = pKinaseCloneHMM.getReferenceAnnotation(i);
+
+ assertEquals(annotation1, annotation2);
+
+ annotation1 = pKinaseHMM.getConsensusResidue(i);
+ annotation2 = pKinaseCloneHMM.getConsensusResidue(i);
+
+ assertEquals(annotation1, annotation2);
+ }
+
+ }
+
+ }
+
+ @Test(priority = 1)
+ public void testGetFilePropertiesAsString() throws FileNotFoundException
+ {
+ String string = fn3.getFilePropertiesAsString();
+
+ Scanner testScanner = new Scanner(string);
+
+ String[] expected = new String[] { "HMMER3/f [3.1b1 | May 2013]",
+ "NAME fn3", "ACC PF00041.13",
+ "DESC Fibronectin type III domain", "LENG 86", "ALPH amino",
+ "RF no", "MM no", "CONS yes", "CS yes", "MAP yes",
+ "DATE Fri Jun 20 08:22:31 2014", "NSEQ 106", "EFFN 11.415833",
+ "CKSUM 3564431818", "GA 8.00 7.20", "TC 8.00 7.20",
+ "NC 7.90 7.90", "STATS LOCAL MSV -9.4043 0.71847",
+ "STATS LOCAL VITERBI -9.7737 0.71847",
+ "STATS LOCAL FORWARD -3.8341 0.71847" };
+
+ for (String value : expected)
+ {
+ assertEquals(testScanner.nextLine(), value);
+ }
+
+ testScanner.close();
+ }
+
+ @Test(priority = 2)
+ public void testGetModelAsString() throws FileNotFoundException
+ {
+ String string = fn3.getModelAsString();
+
+ assertEquals(findValue(2, 2, 2, string), "4.42225");
+ assertEquals(findValue(12, 14, 1, string), "2.79307");
+ assertEquals(findValue(6, 24, 3, string), "0.48576");
+ assertEquals(findValue(19, 33, 2, string), "4.58477");
+ assertEquals(findValue(20, 64, 2, string), "3.61505");
+ assertEquals(findValue(3, 72, 3, string), "6.81068");
+ assertEquals(findValue(10, 80, 2, string), "2.69355");
+ assertEquals(findValue(16, 65, 1, string), "2.81003");
+ assertEquals(findValue(14, 3, 1, string), "2.69012");
+ assertEquals(findValue(11, 32, 1, string), "4.34805");
+
+ }
+
+ /**
+ *
+ * @param symbolIndex
+ * index of symbol being searched. First symbol has index 1.
+ * @param nodeIndex
+ * index of node being searched. Begin node has index 0. First node
+ * has index 1.
+ * @param line
+ * index of line being searched in node. First line has index 1.
+ * @param model
+ * string model being searched
+ * @return value at specified position
+ */
+
+ public String findValue(int symbolIndex, int nodeIndex, int line,
+ String model)
+ {
+
+ String value = "";
+ String current;
+ Scanner scanner = new Scanner(model);
+ current = scanner.nextLine();
+ current = scanner.nextLine();
+
+ for (int lineIndex = 0; lineIndex < line - 1; lineIndex++)
+ {
+ current = scanner.nextLine();
+ }
+ for (int node = 0; node < nodeIndex; node++)
+ {
+ current = scanner.nextLine();
+ current = scanner.nextLine();
+ current = scanner.nextLine();
+ }
+
+ for (int symbol = 0; symbol < symbolIndex; symbol++)
+ {
+ value = scanner.next();
+ if ("COMPO".equals(value))
+ {
+ current = scanner.next();
+ }
+ else if (value.length() < 7)
+ {
+ current = scanner.next();
+ }
+
+ }
+ scanner.close();
+ return value;
+
+ }
+
+ public boolean checkIfListsAreIdentical(List<Double> list1,
+ List<Double> list2)
+ {
+ boolean isDifferent = false;
+ for (int i = 0; i < list1.size(); i++)
+ {
+ Double entry1;
+ Double entry2;
+ entry1 = list1.get(i);
+ entry2 = list2.get(i);
+ if (!(entry1 == entry2))
+ {
+ isDifferent = true;
+ }
+ }
+ return isDifferent;
+ }
+
+}
+
--- /dev/null
+HMMER3/f [3.1 | February 2013]
+NAME MADE1
+ACC DF0000629.2
+DESC MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
+LENG 80
+MAXL 426
+ALPH DNA
+RF yes
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Tue Feb 19 20:33:41 2013
+NSEQ 1997
+EFFN 3.911818
+CKSUM 3015610723
+GA 2.324 4.234
+TC 2.343 1.212
+NC 2.354 5.456
+STATS LOCAL MSV -8.5786 0.71858
+STATS LOCAL VITERBI -9.3632 0.71858
+STATS LOCAL FORWARD -3.4823 0.71858
+HMM A C G T
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.24257 1.59430 1.62906 1.16413
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03960 3.94183 3.94183 1.46634 0.26236 0.00000 *
+ 1 2.69765 2.44396 2.81521 0.24089 1 t x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03960 3.94183 3.94183 1.46634 0.26236 1.09861 0.40547
+ 2 2.72939 2.37873 2.85832 0.24244 2 t x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03725 4.00179 4.00179 1.46634 0.26236 1.09861 0.40547
+ 3 0.16099 3.16370 2.87328 2.99734 3 a x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03604 4.03416 4.03416 1.46634 0.26236 1.09861 0.40547
+ 4 1.98862 2.42132 0.42649 2.10770 4 g x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03539 4.05203 4.05203 1.46634 0.26236 1.09861 0.40547
+ 5 1.96369 2.69532 0.36534 2.32099 5 g x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03764 4.06427 3.92372 1.46634 0.26236 1.09861 0.40547
+ 6 2.56994 2.11239 2.71946 0.30571 6 t x - -
+ 1.37159 1.41129 1.39124 1.37159
+ 0.03806 3.89715 4.07214 1.50442 0.25122 1.00714 0.45454
+ 7 2.58388 2.10353 2.64646 0.31253 12 t x - -
+ 1.38764 1.38524 1.38764 1.38465
+ 0.03494 4.03864 4.09125 1.40070 0.28293 1.09237 0.40860
+ 8 2.18552 2.70201 0.28821 2.64645 14 g x - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03628 4.09157 3.96779 1.46634 0.26236 1.09861 0.40547
+ 9 2.16916 2.82142 0.28427 2.60854 15 g x - -
+ 1.38091 1.39033 1.38365 1.39033
+ 0.03566 4.00237 4.08886 1.38021 0.28972 1.01958 0.44745
+ 10 2.45517 2.15232 2.42886 0.34277 18 t x - -
+ 1.39065 1.39065 1.39065 1.37335
+ 0.03536 4.01212 4.09576 1.39554 0.28462 1.09775 0.40589
+ 11 2.10260 2.95484 0.28160 2.64222 21 g x - -
+ 1.36740 1.40555 1.40555 1.36740
+ 0.03843 3.92069 4.02468 1.44733 0.26814 1.09856 0.40549
+ 12 2.54740 0.30185 2.61355 2.21647 26 c x - -
+ 1.38748 1.38276 1.38748 1.38748
+ 0.03457 4.05446 4.09623 1.40847 0.28040 1.05496 0.42803
+ 13 0.28443 2.72003 2.32214 2.48149 28 a x - -
+ 1.38740 1.38740 1.38298 1.38740
+ 0.03441 4.05976 4.10001 1.41198 0.27926 1.09780 0.40587
+ 14 0.29412 2.55413 2.49679 2.35701 30 a x - -
+ 1.38194 1.39067 1.38194 1.39067
+ 0.03505 4.02482 4.10005 1.39522 0.28473 1.09929 0.40512
+ 15 0.18837 2.99710 2.82270 2.77556 33 a x - -
+ 1.39015 1.39472 1.37503 1.38539
+ 0.03725 3.97815 4.02618 1.37955 0.28994 1.10102 0.40426
+ 16 0.50816 2.05151 2.22111 1.82407 37 a x - -
+ 1.36727 1.38730 1.39683 1.39405
+ 0.04830 3.89881 3.61610 1.29026 0.32186 1.05306 0.42905
+ 17 2.11260 2.73141 0.29747 2.64152 41 g x - -
+ 1.36913 1.40376 1.40376 1.36913
+ 0.03705 3.93681 4.08299 1.44872 0.26771 1.07479 0.41759
+ 18 2.24459 1.90539 2.34054 0.43234 46 t x - -
+ 1.33632 1.42493 1.39937 1.38665
+ 0.04427 3.64574 4.06297 1.70501 0.20061 1.21309 0.35279
+ 19 0.44322 2.17202 2.18055 2.03175 57 a x - -
+ 1.41047 1.41471 1.36338 1.35797
+ 0.03970 3.81957 4.07540 1.65588 0.21186 1.22788 0.34660
+ 20 0.33340 2.42691 2.40824 2.25160 66 a x - -
+ 1.29389 1.44615 1.37917 1.43324
+ 0.04223 3.70146 4.09459 1.55158 0.23815 1.05880 0.42598
+ 21 2.50563 1.98543 2.69601 0.33746 74 t x - -
+ 1.39462 1.39462 1.42862 1.32990
+ 0.04184 3.80216 3.98177 1.80466 0.17976 1.00279 0.45705
+ 22 2.54484 1.97505 2.66483 0.33806 84 t x - -
+ 1.39134 1.39489 1.38662 1.37246
+ 0.03877 3.97504 3.95038 1.37620 0.29107 1.13932 0.38572
+ 23 2.10159 2.83856 0.29282 2.61635 88 g x - -
+ 1.39682 1.39682 1.35536 1.39682
+ 0.05046 3.75402 3.65808 1.08330 0.41321 1.13019 0.39004
+ 24 2.25298 0.61854 2.50691 1.29221 90 c x - -
+ 1.35803 1.49605 1.46737 1.24379
+ 0.06091 3.28322 3.83564 1.89752 0.16245 1.28788 0.32276
+ 25 1.27819 2.23285 0.76242 1.91259 106 g x - -
+ 1.29024 1.67349 1.68279 1.04597
+ 0.05752 3.44263 3.73311 2.58671 0.07825 1.26818 0.33037
+ 26 1.86925 2.58352 0.39466 2.33986 131 g x - -
+ 1.31084 1.49412 1.46666 1.29002
+ 0.04698 3.54257 4.07715 2.25245 0.11109 0.86163 0.54900
+ 27 2.38297 1.93394 2.39162 0.39800 151 t x - -
+ 1.33582 1.47359 1.44163 1.30411
+ 0.04951 3.48445 4.03783 2.15951 0.12260 1.21681 0.35122
+ 28 2.41717 2.17810 2.62774 0.32113 170 t x - -
+ 1.36805 1.48060 1.37439 1.32840
+ 0.04849 3.50958 4.05014 2.58370 0.07850 1.22399 0.34822
+ 29 2.57764 2.35132 2.56552 0.28512 194 t x - -
+ 1.43829 1.43458 1.24787 1.43829
+ 0.04667 3.56670 4.05428 2.49706 0.08591 1.23744 0.34267
+ 30 2.47248 2.07688 2.62257 0.33172 215 t x - -
+ 1.25120 1.52623 1.70635 1.15531
+ 0.08932 3.31524 3.01336 2.81842 0.06156 1.22909 0.34610
+ 31 2.25937 2.13157 2.02027 0.43957 248 t x - -
+ 1.18172 1.43522 1.72841 1.28150
+ 0.07936 2.93117 3.77395 2.46269 0.08906 0.60457 0.79034
+ 32 2.04508 2.84981 0.30490 2.58263 280 g x - -
+ 1.17665 1.66785 1.66218 1.16056
+ 0.05998 3.23615 3.96853 2.83684 0.06040 1.01952 0.44749
+ 33 2.45103 0.38098 2.56776 1.87147 317 c x - -
+ 1.24153 1.52524 1.60663 1.22783
+ 0.05538 3.39046 3.90294 2.73920 0.06680 1.18729 0.36391
+ 34 2.22082 0.36258 2.75077 2.02704 347 c x - -
+ 1.15008 1.62014 1.86511 1.10673
+ 0.06086 3.18178 4.04341 2.94504 0.05403 1.25991 0.33363
+ 35 0.27033 2.66664 2.52541 2.43767 388 a x - -
+ 1.24951 1.47565 1.41392 1.42074
+ 0.07123 3.00373 3.95552 3.13655 0.04440 1.28173 0.32512
+ 36 2.83107 2.41670 2.97197 0.22235 439 t x - -
+ 1.37071 1.57683 1.38637 1.23972
+ 0.05293 3.45216 3.91807 2.54402 0.08181 1.14651 0.38235
+ 37 2.52322 2.25084 2.45909 0.31611 465 t x - -
+ 1.26335 1.55077 1.59008 1.19965
+ 0.07504 3.13329 3.55006 3.08962 0.04659 1.13108 0.38962
+ 38 0.45807 2.30687 1.98940 2.03143 512 a x - -
+ 1.15472 1.67511 1.53797 1.26320
+ 0.09820 3.13076 2.99876 2.79197 0.06326 1.39915 0.28343
+ 39 2.37471 0.42180 2.44763 1.80427 550 c x - -
+ 1.23785 1.49058 1.48364 1.35502
+ 0.06081 3.19472 4.01643 2.41851 0.09327 0.94671 0.49105
+ 40 2.32826 1.95481 2.36781 0.40458 578 t x - -
+ 1.36586 1.46001 1.43000 1.29720
+ 0.05257 3.39673 4.03256 1.84862 0.17133 1.40979 0.27997
+ 41 2.68669 2.13935 2.81520 0.28200 592 t x - -
+ 1.34965 1.42793 1.45781 1.31633
+ 0.04735 3.57826 3.99988 2.09424 0.13144 1.22129 0.34934
+ 42 2.55904 2.16444 2.70859 0.29952 609 t x - -
+ 1.12072 1.61936 1.63578 1.26895
+ 0.07346 3.25910 3.42962 2.85641 0.05919 1.38363 0.28857
+ 43 1.99923 1.61027 2.26343 0.57851 646 t x - -
+ 1.32290 1.58747 1.61095 1.11018
+ 0.06656 3.08568 3.97944 2.44774 0.09046 0.75593 0.63407
+ 44 0.23887 2.79899 2.55209 2.60783 675 a x - -
+ 1.18557 1.50323 1.59070 1.31590
+ 0.05597 3.38637 3.88222 2.46900 0.08847 1.27945 0.32599
+ 45 0.29593 2.53488 2.53903 2.32335 701 a x - -
+ 1.08710 1.54222 1.59276 1.40430
+ 0.07539 2.94521 3.91062 1.91623 0.15918 1.22327 0.34852
+ 46 2.58352 2.40524 2.76700 0.25955 725 t x - -
+ 1.19685 1.58503 1.74852 1.14293
+ 0.06124 3.18279 4.02089 2.82961 0.06085 1.05474 0.42814
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+ 0.02045 3.90014 * 1.46634 0.26236 0.00000 *
+//
--- /dev/null
+HMMER3/e [3.0 | March 2010]
+NAME Pkinase
+ACC PF00069.17
+DESC Protein kinase domain
+LENG 260
+ALPH amino
+RF no
+CONS yes
+CS yes
+MAP yes
+DATE Thu Jun 16 11:44:06 2011
+NSEQ 54
+EFFN 3.358521
+CKSUM 3106786190
+GA 70.30 70.30
+TC 70.30 70.30
+NC 70.20 70.20
+STATS LOCAL MSV -10.7215 0.70254
+STATS LOCAL VITERBI -11.6541 0.70254
+STATS LOCAL FORWARD -5.2305 0.70254
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 2.60017 4.19886 2.94089 2.63789 3.35087 2.89119 3.48337 2.79435 2.60265 2.43454 3.62613 3.06133 3.41286 3.09693 2.94507 2.65650 2.87761 2.67871 4.54052 3.43274
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+ 0.00990 5.01631 5.73865 0.61958 0.77255 0.00000 *
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+ 0.00667 5.01308 * 0.61958 0.77255 0.00000 *
+//
--- /dev/null
+HMMER3/e [3.0 | March 2010]
+NAME Pkinase
+ACC PF00069.17
+DESC Protein kinase domain
+LENG 260
+ALPH amino
+RF no
+MM no
+CONS yes
+CS yes
+MAP yes
+DATE Thu Jun 16 11:44:06 2011
+NSEQ 54
+EFFN 3.358521
+CKSUM 3106786190
+GA 70.30 70.30
+TC 70.30 70.30
+NC 70.20 70.20
+STATS LOCAL MSV -10.7215 0.70254
+STATS LOCAL VITERBI -11.6541 0.70254
+STATS LOCAL FORWARD -5.2305 0.70254
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 2.60017 4.19886 2.94089 2.63789 3.35087 2.89119 3.48337 2.79435 2.60265 2.43454 3.62613 3.06133 3.41286 3.09693 2.94507 2.65650 2.87761 2.67871 4.54052 3.43274
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+//
\ No newline at end of file
--- /dev/null
+HMMER3/f [3.1b1 | May 2013]
+NAME fn3
+ACC PF00041.13
+DESC Fibronectin type III domain
+LENG 86
+ALPH amino
+RF no
+MM no
+CONS yes
+CS yes
+MAP yes
+DATE Fri Jun 20 08:22:31 2014
+NSEQ 106
+EFFN 11.415833
+CKSUM 3564431818
+GA 8.00 7.20
+TC 8.00 7.20
+NC 7.90 7.90
+STATS LOCAL MSV -9.4043 0.71847
+STATS LOCAL VITERBI -9.7737 0.71847
+STATS LOCAL FORWARD -3.8341 0.71847
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 2.70330 4.91262 3.03272 2.64079 3.60307 2.84344 3.74204 3.07942 2.79841 2.65364 4.14864 2.95826 2.87120 3.02176 2.96125 2.44783 2.59757 2.57680 4.02726 3.21526
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+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.00000 *
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+ 0.29928 1.35852 6.43163 0.48724 0.95274 1.77816 0.18506
+ 82 2.84273 4.18992 3.05053 2.12883 3.36284 2.75189 4.25559 3.03507 2.66396 2.65563 4.59024 2.63081 3.84786 2.76844 3.19058 2.84597 2.82776 2.89016 3.06821 3.41272 117 e - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00494 5.70928 6.43163 0.61958 0.77255 1.56406 0.23482
+ 83 3.37920 5.61493 3.74277 3.20384 4.92800 1.01625 3.96683 4.35082 2.94708 2.91738 4.72998 3.71516 3.70329 3.52945 3.00683 1.61777 3.61882 4.00263 6.13360 4.80162 118 g - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00481 5.73459 6.45693 0.61958 0.77255 0.30535 1.33510
+ 84 2.58463 5.93784 3.04102 2.09605 4.57465 2.51630 3.24109 4.26208 2.60545 3.44607 3.62705 3.20484 1.89678 2.68661 2.74662 2.97880 3.02092 3.23569 6.37074 4.50367 119 p - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00361 6.02233 6.74467 0.61958 0.77255 0.28862 1.38348
+ 85 2.48488 5.72055 3.87501 1.97538 3.04853 3.48010 4.51877 3.51898 2.88839 2.73568 4.42660 3.64380 2.08811 3.48814 2.70856 2.40769 2.92982 4.05679 2.77386 3.43366 120 e - - B
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00338 6.08833 6.81068 0.61958 0.77255 0.48576 0.95510
+ 86 3.03720 5.94099 3.75455 2.96917 5.26587 2.91682 3.66571 4.11840 2.98472 4.23738 4.98891 3.74380 4.66031 3.40955 3.12788 0.72443 2.46104 4.32115 6.38683 4.99111 121 s - - E
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00227 6.08723 * 0.61958 0.77255 0.00000 *
+//
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.Test;
+
+public class HMMERColourSchemeTest {
+ HMMERColourScheme scheme = new HMMERColourScheme();
+
+ @Test
+ public void testFindColour() throws MalformedURLException, IOException
+ {
+
+ HMMFile file = new HMMFile(new FileParse(
+ "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
+
+ scheme.hmm = file.getHMM();
+ Color expected;
+
+ Color actual = scheme.findColour('A', 1, null, null, 0);
+ assertEquals(actual, Color.ORANGE);
+
+ actual = scheme.findColour('Y', 3, null, null, 0);
+ assertEquals(actual, Color.ORANGE);
+
+ actual = scheme.findColour('M', 109, null, null, 0);
+ expected = new Color(230, 0, 0);
+ assertEquals(actual, expected);
+
+ actual = scheme.findColour('I', 6, null, null, 0);
+ expected = new Color(171, 171, 255);
+ assertEquals(actual, expected);
+
+ actual = scheme.findColour('V', 14, null, null, 0);
+ expected = new Color(129, 129, 255);
+ assertEquals(actual, expected);
+
+ actual = scheme.findColour('X', 100000000, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+
+
+ }
+
+}
--- /dev/null
+1.8, 4.53
+3.4, 2.65
+0, 5.4
+6.4, 10.8
\ No newline at end of file
--- /dev/null
+package jalview.util;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
+public class HMMProbabilityDistributionAnalyserTest {
+
+ HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
+
+ @Test
+ public void testMoveToFile() throws IOException
+ {
+
+ BufferedReader br = new BufferedReader(new FileReader(
+ "test/jalview/util/test_Fams_for_probability_analysis"));
+ analyser.moveLocationBy(1, br);
+
+ String line = br.readLine();
+ assertEquals(line, "# STOCKHOLM 1.0");
+ line = br.readLine();
+ assertEquals(line, "seq1 ATW");
+ line = br.readLine();
+ assertEquals(line, "seq2 ATI");
+
+ }
+
+ @Test
+ public void testCountValidResidues()
+ {
+ analyser.sequences = new Vector<>();
+ analyser.hmm = new HiddenMarkovModel();
+ analyser.hmm.addFileProperty("LENG", "8");
+
+ List<HMMNode> nodes = new ArrayList<>();
+ nodes.add(new HMMNode());
+ for (int i = 1; i < 9; i++)
+ {
+ HMMNode node = new HMMNode();
+ node.setAlignmentColumn(i - 1);
+ nodes.add(node);
+
+ }
+ analyser.hmm.setNodes(nodes);
+
+ SequenceI[] sequence = new Sequence[] {
+ new Sequence("seq1", "ATGWWSCF"), new Sequence("seq2", "GGMKI"),
+ new Sequence("seq3", "--.ATccGc") };
+ analyser.sequences.add(sequence[0]);
+ analyser.sequences.add(sequence[1]);
+ analyser.sequences.add(sequence[2]);
+
+ int count = analyser.countValidResidues();
+ assertEquals(count, 16);
+ }
+
+ @Test(priority = 0)
+ public void testReadBinned() throws IOException
+ {
+ analyser.readBinned("test/jalview/util/");
+ Map<String, Double> map = analyser.binned;
+ assertEquals(map.get("1.8"), 4.53);
+ assertEquals(map.get("3.4"), 2.65);
+ assertEquals(map.get("6.4"), 10.8);
+ assertEquals(map.get("0"), 5.4);
+ }
+
+ @Test
+ public void testReadRaw() throws IOException
+ {
+ analyser.readRaw("test/jalview/util/");
+ List<ArrayList<Double>> list = analyser.raw;
+
+ assertEquals(list.get(0).get(0), 1.43);
+ assertNull(list.get(0).get(2));
+ assertEquals(list.get(1).get(1), 1.2);
+ assertEquals(list.get(2).get(0), 5.6);
+ assertEquals(list.get(2).get(2), 6.8);
+
+ }
+
+ @Test(priority = 1)
+ public void testProcessData() throws IOException
+ {
+ analyser.keepRaw = true;
+ BufferedReader brFam = new BufferedReader(new FileReader(
+ "test/jalview/util/test_Fams_for_probability_analysis"));
+ BufferedReader brHMM = new BufferedReader(new FileReader(
+ "test/jalview/util/test_HMMs_for_probability_analysis"));
+ analyser.readStockholm(brFam);
+ analyser.readHMM(brHMM);
+ analyser.processData(6);
+ Map<String, Double> map = analyser.binned;
+ List<ArrayList<Double>> list = analyser.raw;
+ assertEquals(map.get("1.8"), 4.863, 0.001d);
+ assertEquals(map.get("3.4"), 2.65);
+ assertEquals(map.get("0"), 5.4);
+ assertEquals(map.get("6.4"), 10.8);
+ assertEquals(map.get("1.4"), 0.166667, 0.00001d);
+ assertEquals(map.get("4.4"), 0.5);
+
+ }
+}
--- /dev/null
+Seq1, Seq2, Seq3
+1.43, 2.34, 5.6,
+EMPTY, 1.2, 0.05,
+EMPTY, 5.4, 6.8,
\ No newline at end of file
--- /dev/null
+# STOCKHOLM 1.0
+seq1 AW
+seq2 GW
+seq3 AW
+//
+# STOCKHOLM 1.0
+seq1 ATW
+seq2 ATI
+//
+# STOCKHOLM 1.0
+seq1 R-WW
+seq2 RAWW
+//
\ No newline at end of file
--- /dev/null
+HMMER3/f [3.1b2 | February 2015]
+NAME test1
+LENG 4
+ALPH amino
+RF no
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Fri Jul 21 06:35:06 2017
+NSEQ 3
+EFFN 3.000000
+CKSUM 657102310
+STATS LOCAL MSV -5.0223 0.82341
+STATS LOCAL VITERBI -4.9569 0.82341
+STATS LOCAL FORWARD -2.0282 0.82341
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.94296 5.20658 4.78882 4.52987 4.66525 2.54188 5.19553 2.25221 4.08549 3.87133 5.00250 4.55734 4.73106 4.65220 2.77287 3.67799 1.53923 3.75384 1.48526 4.84023
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.00000 *
+ 1 0.67027 4.79120 4.60974 4.51892 5.43734 1.28080 5.43621 4.90028 4.64310 4.61059 5.39837 4.28688 4.41468 4.80804 4.79047 3.08135 3.44468 4.10506 6.74908 5.67939 1 A - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510
+ 2 5.43405 6.34487 5.85697 5.84679 4.39288 5.10370 5.65594 5.70664 5.69821 4.87848 6.25251 5.89664 5.70261 6.00722 5.60902 5.64576 5.80049 5.59366 0.08910 4.36301 2 W - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510
+ 3 3.42384 5.23617 4.84601 4.77568 5.39247 4.01365 5.64153 4.72950 4.75585 4.52264 5.55782 4.69647 4.81267 5.08969 4.87301 3.64217 0.20934 4.25217 6.65833 5.63018 3 T - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01083 4.92694 5.64929 0.61958 0.77255 0.48576 0.95510
+ 4 3.53954 5.09963 4.71395 4.06038 4.20429 4.44020 4.65482 0.90152 3.16536 2.96072 4.13056 4.31689 4.83725 3.95143 1.46549 3.86829 3.78084 2.85654 5.74911 4.54685 4 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00730 4.92341 * 0.61958 0.77255 0.00000 *
+//
+HMMER3/f [3.1b2 | February 2015]
+NAME test2
+LENG 3
+ALPH amino
+RF no
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Fri Jul 21 06:36:50 2017
+NSEQ 2
+EFFN 2.000000
+CKSUM 777554360
+STATS LOCAL MSV -5.2452 0.95763
+STATS LOCAL VITERBI -5.2886 0.95763
+STATS LOCAL FORWARD -1.5134 0.95763
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.33364 4.79082 4.44132 4.24796 3.91456 3.75718 4.85762 2.23342 4.16821 3.09137 4.29744 4.25088 4.41741 4.46803 4.31080 3.33397 1.39376 3.21010 2.54819 4.14914
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.00000 *
+ 1 0.32372 4.76536 4.42980 4.32857 5.00499 3.55951 5.22620 4.27004 4.37081 4.10495 5.08789 4.22499 4.36948 4.63911 4.51684 3.12947 3.46009 3.76842 6.33337 5.25783 1 A - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.48576 0.95510
+ 2 3.04414 4.87155 4.35068 4.21532 4.89213 3.66881 5.13994 4.14202 4.17893 3.96810 5.00600 4.23490 4.44590 4.53729 4.35178 3.25814 0.35496 3.73038 6.23308 5.12388 2 T - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.48576 0.95510
+ 3 3.41901 4.77187 4.98694 4.49106 3.10447 4.49364 4.52024 1.21391 4.22709 2.30875 3.57865 4.53952 4.83367 4.43564 4.31127 3.88439 3.66452 2.61326 1.44329 3.34125 3 i - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 4.62006 * 0.61958 0.77255 0.00000 *
+//
+HMMER3/f [3.1b2 | February 2015]
+NAME test3
+LENG 4
+ALPH amino
+RF no
+MM no
+CONS yes
+CS no
+MAP yes
+DATE Fri Jul 21 06:37:01 2017
+NSEQ 2
+EFFN 2.000000
+CKSUM 986955970
+STATS LOCAL MSV -5.4578 0.80004
+STATS LOCAL VITERBI -5.2499 0.80004
+STATS LOCAL FORWARD -2.1856 0.80004
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 2.16700 5.33023 4.57707 4.32329 4.15728 4.03215 4.83242 4.49728 3.73978 4.00181 5.18156 4.45520 4.63709 4.41734 1.53081 3.84281 4.10073 4.20172 0.82417 4.15750
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.00000 *
+ 1 4.09153 5.75008 4.67229 4.09411 5.31638 4.34678 4.67762 4.97541 2.93879 4.35023 5.37643 4.37234 4.85576 3.90366 0.27042 4.17197 4.33362 4.67489 6.11461 5.14175 1 R - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.39762 4.62483 1.14482 0.61958 0.77255 0.48576 0.95510
+ 2 0.58385 4.42717 3.89187 3.72118 4.47383 3.23815 4.69159 3.65968 3.74862 3.52210 4.52478 3.76053 4.01438 4.05655 3.96007 2.78076 3.08518 3.24526 5.86063 4.71068 2 A - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.02145 4.24866 4.97100 0.61958 0.77255 0.27360 1.42978
+ 3 4.82318 5.87391 5.36844 5.28961 3.81117 4.70308 5.10523 4.98084 5.06729 4.21822 5.56037 5.33222 5.28501 5.40387 5.04111 5.02415 5.17266 4.88017 0.16601 3.78547 3 W - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.01467 4.62483 5.34718 0.61958 0.77255 0.48576 0.95510
+ 4 4.82318 5.87391 5.36844 5.28961 3.81117 4.70308 5.10523 4.98084 5.06729 4.21822 5.56037 5.33222 5.28501 5.40387 5.04111 5.02415 5.17266 4.88017 0.16601 3.78547 4 W - - -
+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503
+ 0.00990 4.62006 * 0.61958 0.77255 0.00000 *
+//
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff