--- /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 *
+//
<mapID target="alwCalc" url="html/menus/alwcalculate.html"/>
<mapID target="wsMenu" url="html/menus/wsmenu.html"/>
+ <mapID target="alwHmmer" url="html/menus/alwhmmer.html"/>
<mapID target="popMenu" url="html/menus/popupMenu.html"/>
<mapID target="popMenuAddref" url="html/menus/popupMenu.html#addrefannot"/>
<mapID target="annotPanelMenu" url="html/menus/alwannotationpanel.html"/>
<tocitem text="Colour Menu" target="alwColour" />
<tocitem text="Calculate Menu" target="alwCalc" />
<tocitem text="Web Service Menu" target="wsMenu" />
+ <tocitem text="HMMER Menu" target="alwHmmer" />
<tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
<tocitem text="Popup Menu" target="popMenu" />
</tocitem>
sequence alignments and EPS files.
</li>
<li>The <a href="#editing"><strong>"Editing"</strong>
- Preferences</a> tab contains settings affecting the export of
- sequence alignments and EPS files.
+ Preferences</a> tab contains settings affecting the behaviour of alignments as you edit them.
+ </li>
+ <li>The <a href="#hmmer"><strong>"HMMER"</strong>
+ Preferences</a> tab allows you to configure locally installed HMMER tools.
</li>
<li>The <a href="dassettings.html"><strong>"DAS
Settings"</strong> Preferences</a> tab allows you to select which DAS
<em>Sort with New Tree</em> - When selected, any trees calculated or
loaded onto the alignment will automatically sort the alignment.
</p>
- <p> </p>
- <p> </p>
+ <p>
+ <a name="hmmer"><strong>"HMMER" Preferences tab</strong></a>
+ </p>
+ <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
+ then you should specify on this screen the location of the installation (the path to the folder
+ containing binary executable programs). Double-click in the input field to open a file browser.</p>
+ <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
+ enabled in the Alignment window.</p>
</body>
</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+</head>
+<body>
+<p>
+ <strong>HMMER Menu</strong>
+</p>
+<p>This menu is available if hmmbuild tools have been installed and configured in the
+<a href="../features/preferences.html#hmmer">HMMER Preferences</a> panel.
+ <br><br>
+
+ <strong>hmmbuild</strong>
+ <br><br>Run hmmbuild to create a Hidden Markov Model profile of your sequence alignment or sub-groups.
+ <br><br>The consensus sequence for the computed profile is inserted as the first sequence of
+ the alignment (or group) for which hmmbuild is run.
+ <br>Jalview also computes and displays an annotation below the alignment, showing
+ the information content of each column.
+ <br>This is calculated as the sum over residue symbols of
+ <pre>
+ match emission probability * log(match emission probability / background frequency) / log(2)
+ </pre>
+ where the background frequencies are taken from (tbc: where? not https://www.ebi.ac.uk/uniprot/TrEMBLstats)
+ <ul>
+ <li>Edit settings and run...
+ <br><br>Choose whether to run hmmbuild for the whole alignment, or all or selected groups, or both
+ (default is the alignment).
+ <br>Optionally enter a name to give the HMM profile consensus sequence
+ (default is "Alignment" or group name, with "_HMM" appended).
+ <br>Use Reference Annotation: select this option if your alignment has an RF reference annotation,
+ and you wish to constrain the HMM profile to it (hmmbuild option '--hand').
+ <br><br></li>
+ <li>hmmbuild with default settings
+ <br><br>Runs hmmbuild for the whole alignment.</li>
+ </ul>
+
+ <strong>hmmalign</strong> and <strong>hmmsearch</strong> require an HMM consensus sequence to be selected first.
+ <br><em>To do this, right-click on the name of an HMM sequence added by hmmbuild, and 'Select HMM'.
+ The alignment will be with respect to the HMM profile for the consensus sequence.</em>
+ <br><br>
+ <strong>hmmalign</strong>
+ <br><br>Run hmmalign to align selected sequences (or the whole alignment) to a selected HMM profile.
+ <ul>
+ <li>Edit settings and run...
+ <br><br>Choose whether to 'trim non-matching termini' - hmmalign option '--trim'.
+ <br><br></li>
+ <li>hmmalign with default settings</li>
+ </ul>
+ <strong>hmmsearch</strong>
+ <br><br>Run hmmsearch to use an HMM profile as input to search a sequence database.
+ <ul>
+ <li>Edit settings and run...
+ <ul>
+ <li>tbc: choose database</li>
+ <li>tbc: automatically align</li>
+ <li>tbc: return accessions</li>
+ <li>tbc: number of results</li>
+ <li>tbc: sequence eValue cutoff</li>
+ <li>tbc: domains eValue cutoff</li>
+ </ul>
+ </li>
+ <br><li>hmmsearch with default settings</li>
+ <br><li>Add database
+ <br>Browse to select a local sequence data file to be searched</li>
+ </ul>
+<br>
+</body>
+</html>
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
label.colourScheme_nucleotide = Nucleotide
label.colourScheme_t-coffee_scores = T-Coffee Scores
label.colourScheme_rna_helices = By RNA Helices
+label.colourScheme_hmmer-uniprot = HMMER profile v global background
+label.colourScheme_hmmer-alignment = HMMER profile v alignment background
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
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.most_polymer_residues = Most Polymer Residues
label.cached_structures = Cached Structures
label.free_text_search = Free Text Search
+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.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
+warn.no_selected_hmm = Please select a hidden Markov model sequence.
+label.select_hmm = Select HMM
+warn.no_sequence_data = No sequence data found.
+warn.empty_grp_or_alignment = An empty group or alignment was found.
+label.no_sequences_found = No matching sequences, or an error occurred.
+label.hmmer = HMMER
+label.trim_termini = Trim Non-Matching Termini
+label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed.
+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.hmm_command_failed = hmm command 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
+label.hmmer_no_sequences_found = No sequences found
+label.number_of_results = Number of Results to Return
+label.auto_align_seqs = Automatically Align Fetched Sequences
+label.use_accessions = Return Accessions
+label.seq_e_value = Sequence E-value Cutoff
+label.seq_score = Sequence Score Threshold
+label.dom_e_value = Domain E-value Cutoff
+label.dom_score = Domain Score Threshold
+label.number_of_results_desc = The maximum number of results that hmmsearch will return
+label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
+label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequences name
+label.seq_e_value_desc = The E-value cutoff for returned sequences
+label.seq_score_desc = The score threshold for returned sequences
+label.dom_e_value_desc = The E-value cutoff for returned domains
+label.dom_score_desc = The score threshold for returned domains
+label.not_enough_sequences = There are not enough sequences to run {0}
+label.add_database = Add Database
+label.this_alignment = This alignment
+warn.file_not_exists = File does not exist
+warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam.
+label.database_for_hmmsearch = The database hmmsearch will search through
+label.use_reference = Use Reference Annotation
+label.use_reference_desc = If true, hmmbuild will keep all columns defined as a reference position by the reference annotation
+label.hmm_name = HMM Name
+label.hmm_name_desc = The name given to the HMM.
+warn.no_reference_annotation = No reference annotation found.
+label.hmmbuild_for = Build HMM for
+label.hmmbuild_for_desc = Build an HMM for the selected sequence groups.
+label.alignment = Alignment
+label.groups_and_alignment = All groups and alignment
+label.groups = All groups
+label.selected_group = Selected group
+label.use_info_for_height = Use Information Content as Letter Height
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;
* This class is used extensively in calculating alignment colourschemes that
* depend on the amount of conservation in each alignment column.
*
- * @author $author$
- * @version $Revision$
*/
public class AAFrequency
{
- public static final String PROFILE = "P";
-
- /*
- * Quick look-up of String value of char 'A' to 'Z'
- */
- private static final String[] CHARS = new String['Z' - 'A' + 1];
+ private static final double LOG2 = Math.log(2);
- static
- {
- for (char c = 'A'; c <= 'Z'; c++)
- {
- CHARS[c - 'A'] = String.valueOf(c);
- }
- }
+ public static final String PROFILE = "P";
public static final ProfilesI calculate(List<SequenceI> list, int start,
int end)
}
/**
+ * 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
+ * if true, all residue counts are saved (enables profile logo)
+ * @param removeBelowBackground
+ * if true, symbols with a match emission probability less than
+ * background frequency are ignored
+ * @return
+ */
+ public static ProfilesI calculateHMMProfiles(final HiddenMarkovModel hmm,
+ int width, int start, int end, boolean saveFullProfile,
+ boolean removeBelowBackground, boolean infoLetterHeight)
+ {
+ ProfileI[] result = new ProfileI[width];
+ char[] symbols = hmm.getSymbols().toCharArray();
+ int symbolCount = symbols.length;
+ for (int column = start; column < end; column++)
+ {
+ ResidueCount counts = new ResidueCount();
+ for (char symbol : symbols)
+ {
+ int value = getAnalogueCount(hmm, column, symbol,
+ removeBelowBackground, infoLetterHeight);
+ 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 gap count annotation row.
+ * 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 gaprow
+ * @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 float completeInformation(AlignmentAnnotation information,
+ ProfilesI profiles, int startCol, int endCol, long nseq,
+ float currentMax)
+ {
+ // 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 0;
+ }
+
+ float max = 0f;
+ SequenceI hmmSeq = information.sequenceRef;
+ HiddenMarkovModel hmm = hmmSeq.getHMM();
+
+ for (int column = startCol; column < endCol; column++)
+ {
+ ProfileI profile = profiles.get(column);
+ if (profile == null)
+ {
+ /*
+ * happens if sequences calculated over were
+ * shorter than alignment width
+ */
+ information.annotations[column] = null;
+ return 0f;
+ }
+
+ float value = hmm.getInformationContent(column);
+ boolean isNaN = Float.isNaN(value);
+ if (!isNaN)
+ {
+ max = Math.max(max, value);
+ }
+
+ String description = isNaN ? null
+ : String.format("%.4f bits", value);
+ information.annotations[column] = new Annotation(
+ Character.toString(Character
+ .toUpperCase(hmm.getConsensusAtAlignColumn(column))),
+ description, ' ', value);
+ }
+
+ max = Math.max(max, currentMax);
+ information.graphMax = max;
+ return max;
+ }
+
+ /**
+ * Derive the occupancy count annotation
+ *
+ * @param occupancy
* the annotation row to add annotations to
* @param profiles
* the source consensus data
* @param endCol
* end column (exclusive)
*/
- public static void completeGapAnnot(AlignmentAnnotation gaprow,
+ public static void completeOccupancyAnnot(AlignmentAnnotation occupancy,
ProfilesI profiles, int startCol, int endCol, long nseq)
{
- if (gaprow == null || gaprow.annotations == null
- || gaprow.annotations.length < endCol)
+ if (occupancy == null || occupancy.annotations == null
+ || occupancy.annotations.length < endCol)
{
/*
* called with a bad alignment annotation row
return;
}
// always set ranges again
- gaprow.graphMax = nseq;
- gaprow.graphMin = 0;
+ occupancy.graphMax = nseq;
+ occupancy.graphMin = 0;
double scale = 0.8 / nseq;
for (int i = startCol; i < endCol; i++)
{
* happens if sequences calculated over were
* shorter than alignment width
*/
- gaprow.annotations[i] = null;
+ occupancy.annotations[i] = null;
return;
}
String description = "" + gapped;
- gaprow.annotations[i] = new Annotation("", description, '\0', gapped,
+ occupancy.annotations[i] = new Annotation("", description, '\0',
+ gapped,
jalview.util.ColorUtils.bleachColour(Color.DARK_GRAY,
(float) scale * gapped));
}
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 sorted HMM profile for the given column of the alignment. The
+ * returned array contains
+ *
+ * <pre>
+ * [profileType=0, numberOfValues, 100, charValue1, percentage1, charValue2, percentage2, ...]
+ * in descending order of percentage value
+ * </pre>
+ *
+ * @param hmm
+ * @param column
+ * @param removeBelowBackground
+ * if true, ignores residues with probability less than their
+ * background frequency
+ * @param infoHeight
+ * if true, uses the log ratio 'information' measure to scale the
+ * value
+ * @return
+ */
+ public static int[] extractHMMProfile(HiddenMarkovModel hmm, int column,
+ boolean removeBelowBackground, boolean infoHeight)
+ {
+ if (hmm == null)
+ {
+ return null;
+ }
+ String alphabet = hmm.getSymbols();
+ int size = alphabet.length();
+ char symbols[] = new char[size];
+ int values[] = new int[size];
+ int totalCount = 0;
+
+ for (int i = 0; i < size; i++)
+ {
+ char symbol = alphabet.charAt(i);
+ symbols[i] = symbol;
+ int value = getAnalogueCount(hmm, column, symbol,
+ removeBelowBackground, infoHeight);
+ values[i] = value;
+ totalCount += value;
+ }
+
+ /*
+ * sort symbols by increasing emission probability
+ */
+ QuickSort.sort(values, symbols);
+
+ int[] profile = new int[3 + size * 2];
+
+ profile[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
+ profile[1] = size;
+ profile[2] = 100;
+
+ /*
+ * order symbol/count profile by decreasing emission probability
+ */
+ if (totalCount != 0)
+ {
+ int arrayPos = 3;
+ for (int k = size - 1; k >= 0; k--)
+ {
+ Float percentage;
+ int value = values[k];
+ if (removeBelowBackground)
+ {
+ percentage = ((float) value) / totalCount * 100f;
+ }
+ else
+ {
+ percentage = value / 100f;
+ }
+ int intPercent = Math.round(percentage);
+ profile[arrayPos] = symbols[k];
+ profile[arrayPos + 1] = intPercent;
+ arrayPos += 2;
+ }
+ }
+ return profile;
+ }
+
+ /**
+ * Converts the emission probability of a residue at a column in the alignment
+ * to a 'count', suitable for rendering as an annotation value
+ *
+ * @param hmm
+ * @param column
+ * @param symbol
+ * @param removeBelowBackground
+ * if true, returns 0 for any symbol with a match emission
+ * probability less than the background frequency
+ * @infoHeight if true, uses the log ratio 'information content' to scale the
+ * value
+ * @return
+ */
+ static int getAnalogueCount(HiddenMarkovModel hmm, int column,
+ char symbol, boolean removeBelowBackground, boolean infoHeight)
+ {
+ double value = hmm.getMatchEmissionProbability(column, symbol);
+ double freq = ResidueProperties.backgroundFrequencies
+ .get(hmm.getAlphabetType()).get(symbol);
+ if (value < freq && removeBelowBackground)
+ {
+ return 0;
+ }
+
+ if (infoHeight)
+ {
+ value = value * (Math.log(value / freq) / LOG2);
+ }
+
+ value = value * 10000d;
+ return Math.round((float) value);
+ }
}
*/
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;
}
/**
* Updates the display of calculated annotation values (does not recalculate
- * the values). This allows ßquick redraw of annotations when display settings
- * are changed.
+ * the values). This allows a quick redraw of annotations when display
+ * settings are changed.
*/
void updateAnnotation();
*
* @return
*/
- public ViewportRanges getRanges();
+ ViewportRanges getRanges();
/**
* calculate the height for visible annotation, revalidating bounds where
*
* @return total height of annotation
*/
- public int calcPanelHeight();
+ int calcPanelHeight();
/**
* Answers true if the viewport has at least one column selected
boolean isNormaliseSequenceLogo();
+ boolean isShowInformationHistogram();
+
+ boolean isShowHMMSequenceLogo();
+
+ boolean isNormaliseHMMSequenceLogo();
+
ColourSchemeI getGlobalColourScheme();
/**
ColumnSelection getColumnSelection();
- ProfilesI getSequenceConsensusHash();
+ ProfilesI getConsensusProfiles();
/**
* Get consensus data table for the cDNA complement of this alignment (if any)
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
*
* @return
*/
- AlignmentAnnotation getAlignmentGapAnnotation();
+ AlignmentAnnotation getOccupancyAnnotation();
/**
* get the container for cDNA complement consensus annotation
*
* @param hconsensus
*/
- void setSequenceConsensusHash(ProfilesI hconsensus);
+ void setConsensusProfiles(ProfilesI hconsensus);
/**
* Set the cDNA complement consensus for the viewport
*
* @return a copy of this view's current display settings
*/
- public ViewStyleI getViewStyle();
+ ViewStyleI getViewStyle();
/**
* update the view's display settings with the given style set
*
* @param settingsForView
*/
- public void setViewStyle(ViewStyleI settingsForView);
+ void setViewStyle(ViewStyleI settingsForView);
/**
* Returns a viewport which holds the cDna for this (protein), or vice versa,
*/
void setFollowHighlight(boolean b);
- public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+ void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
/**
* check if current selection group is defined on the view, or is simply a
@Override
void setProteinFontAsCdna(boolean b);
- public abstract TreeModel getCurrentTree();
+ void setHmmProfiles(ProfilesI info);
+
+ ProfilesI getHmmProfiles();
+
+ /**
+ * Updates all information annotations.
+ *
+ * @param ap
+ */
+ void updateInformation(AlignmentViewPanel ap);
+
+ boolean isInfoLetterHeight();
+
+ abstract TreeModel getCurrentTree();
- public abstract void setCurrentTree(TreeModel tree);
+ abstract void setCurrentTree(TreeModel tree);
}
alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
+ viewport.updateInformation(alignPanel);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.isFollowHighlight());
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
*
* This file is part of Jalview.
*
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
private AnnotationColumnChooser annotationColumnSelectionState;
+ java.awt.Frame nullFrame;
+
+ protected FeatureSettings featureSettings = null;
+
+ private float heightScale = 1, widthScale = 1;
+
public AlignViewport(AlignmentI al, JalviewLite applet)
{
super(al);
if (colour != null)
{
residueShading = new ResidueShader(
- ColourSchemeProperty.getColourScheme(alignment, colour));
+ ColourSchemeProperty.getColourScheme(getAlignment(),
+ colour));
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(consensusProfiles);
}
}
}
}
initAutoAnnotation();
-
}
- java.awt.Frame nullFrame;
-
- protected FeatureSettings featureSettings = null;
-
- private float heightScale = 1, widthScale = 1;
-
/**
* {@inheritDoc}
*/
// TODO implement for applet
}
+ @Override
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return normaliseHMMSequenceLogo;
+ }
+
}
MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null)
? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus()
+ .isIgnoreGapsConsensus()
: ap.av.isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addItemListener(new ItemListener()
od = new OverviewDimensionsShowHidden(av.getRanges(),
(av.isShowAnnotation()
- && av.getSequenceConsensusHash() != null));
+ && av.getConsensusProfiles() != null));
oviewCanvas = new OverviewCanvas(od, av);
setLayout(new BorderLayout());
}
// always do this - annotation has own state
// but defer colourscheme update until hidden sequences are passed in
- boolean vischange = stretchGroup.recalcConservation(true);
+ boolean vischange = stretchGroup.recalcAnnotations(true);
// here we rely on stretchGroup == av.getSelection()
needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
&& afterDrag;
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
*/
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);
}
private List<SequenceI> sequences;
+ private SequenceI hmmConsensus;
+
protected List<SequenceGroup> groups;
protected char gapCharacter = '-';
}
/**
+ * 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!
}
@Override
+ public SequenceI getHmmConsensus()
+ {
+ return hmmConsensus;
+ }
+
+ @Override
+ public void setHmmConsensus(SequenceI hmmConsensus)
+ {
+ this.hmmConsensus = hmmConsensus;
+ }
+
+ @Override
public void setupJPredAlignment()
{
SequenceI repseq = getSequenceAt(0);
}
}
}
-
}
private long invalidrnastruc = -2;
/**
- * Updates the _rnasecstr field Determines the positions that base pair and
- * the positions of helices based on secondary structure from a Stockholm file
- *
- * @param rnaAnnotation
- */
- private void _updateRnaSecStr(CharSequence rnaAnnotation)
- {
- try
- {
- _rnasecstr = Rna.getHelixMap(rnaAnnotation);
- invalidrnastruc = -1;
- } catch (WUSSParseException px)
- {
- // DEBUG System.out.println(px);
- invalidrnastruc = px.getProblemPos();
- }
- if (invalidrnastruc > -1)
- {
- return;
- }
-
- if (_rnasecstr != null && _rnasecstr.length > 0)
- {
- // show all the RNA secondary structure annotation symbols.
- isrna = true;
- showAllColLabels = true;
- scaleColLabel = true;
- _markRnaHelices();
- }
- // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
-
- }
-
- private void _markRnaHelices()
- {
- int mxval = 0;
- // Figure out number of helices
- // Length of rnasecstr is the number of pairs of positions that base pair
- // with each other in the secondary structure
- for (int x = 0; x < _rnasecstr.length; x++)
- {
-
- /*
- * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
- * this.annotation._rnasecstr[x].getBegin());
- */
- // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
- int val = 0;
- try
- {
- val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
- if (mxval < val)
- {
- mxval = val;
- }
- } catch (NumberFormatException q)
- {
- }
- ;
-
- annotations[_rnasecstr[x].getBegin()].value = val;
- annotations[_rnasecstr[x].getEnd()].value = val;
-
- // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
- // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
- }
- setScore(mxval);
- }
-
- /**
* map of positions in the associated annotation
*/
private Map<Integer, Annotation> sequenceMapping;
}
/**
+ * Copy constructor creates a new independent annotation row with the same
+ * associated sequenceRef
+ *
+ * @param annotation
+ */
+ public AlignmentAnnotation(AlignmentAnnotation annotation)
+ {
+ setAnnotationId();
+ this.label = new String(annotation.label);
+ if (annotation.description != null)
+ {
+ this.description = new String(annotation.description);
+ }
+ this.graphMin = annotation.graphMin;
+ this.graphMax = annotation.graphMax;
+ this.graph = annotation.graph;
+ this.graphHeight = annotation.graphHeight;
+ this.graphGroup = annotation.graphGroup;
+ this.groupRef = annotation.groupRef;
+ this.editable = annotation.editable;
+ this.autoCalculated = annotation.autoCalculated;
+ this.hasIcons = annotation.hasIcons;
+ this.hasText = annotation.hasText;
+ this.height = annotation.height;
+ this.label = annotation.label;
+ this.padGaps = annotation.padGaps;
+ this.visible = annotation.visible;
+ this.centreColLabels = annotation.centreColLabels;
+ this.scaleColLabel = annotation.scaleColLabel;
+ this.showAllColLabels = annotation.showAllColLabels;
+ this.calcId = annotation.calcId;
+ if (annotation.properties != null)
+ {
+ properties = new HashMap<>();
+ for (Map.Entry<String, String> val : annotation.properties.entrySet())
+ {
+ properties.put(val.getKey(), val.getValue());
+ }
+ }
+ if (this.hasScore = annotation.hasScore)
+ {
+ this.score = annotation.score;
+ }
+ if (annotation.threshold != null)
+ {
+ threshold = new GraphLine(annotation.threshold);
+ }
+ Annotation[] ann = annotation.annotations;
+ if (annotation.annotations != null)
+ {
+ this.annotations = new Annotation[ann.length];
+ for (int i = 0; i < ann.length; i++)
+ {
+ if (ann[i] != null)
+ {
+ annotations[i] = new Annotation(ann[i]);
+ if (_linecolour != null)
+ {
+ _linecolour = annotations[i].colour;
+ }
+ }
+ }
+ }
+ if (annotation.sequenceRef != null)
+ {
+ this.sequenceRef = annotation.sequenceRef;
+ if (annotation.sequenceMapping != null)
+ {
+ Integer p = null;
+ sequenceMapping = new HashMap<>();
+ Iterator<Integer> pos = annotation.sequenceMapping.keySet()
+ .iterator();
+ while (pos.hasNext())
+ {
+ // could optimise this!
+ p = pos.next();
+ Annotation a = annotation.sequenceMapping.get(p);
+ if (a == null)
+ {
+ continue;
+ }
+ if (ann != null)
+ {
+ for (int i = 0; i < ann.length; i++)
+ {
+ if (ann[i] == a)
+ {
+ sequenceMapping.put(p, annotations[i]);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ this.sequenceMapping = null;
+ }
+ }
+ // TODO: check if we need to do this: JAL-952
+ // if (this.isrna=annotation.isrna)
+ {
+ // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+ }
+ validateRangeAndDisplay(); // construct hashcodes, etc.
+ }
+
+ /**
+ * copy constructor with edit based on the hidden columns marked in colSel
+ *
+ * @param alignmentAnnotation
+ * @param colSel
+ */
+ public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
+ HiddenColumns hidden)
+ {
+ this(alignmentAnnotation);
+ if (annotations == null)
+ {
+ return;
+ }
+ makeVisibleAnnotation(hidden);
+ }
+
+ /**
+ * Creates a new AlignmentAnnotation object.
+ *
+ * @param label
+ * DOCUMENT ME!
+ * @param description
+ * DOCUMENT ME!
+ * @param annotations
+ * DOCUMENT ME!
+ * @param min
+ * DOCUMENT ME!
+ * @param max
+ * DOCUMENT ME!
+ * @param winLength
+ * DOCUMENT ME!
+ */
+ public AlignmentAnnotation(String label, String description,
+ Annotation[] annotations, float min, float max, int graphType)
+ {
+ setAnnotationId();
+ // graphs are not editable
+ editable = graphType == 0;
+
+ this.label = label;
+ this.description = description;
+ this.annotations = annotations;
+ graph = graphType;
+ graphMin = min;
+ graphMax = max;
+ validateRangeAndDisplay();
+ }
+
+ /**
+ * Score only annotation
+ *
+ * @param label
+ * @param description
+ * @param score
+ */
+ public AlignmentAnnotation(String label, String description, double score)
+ {
+ this(label, description, null);
+ setScore(score);
+ }
+
+ /**
+ * Updates the _rnasecstr field Determines the positions that base pair and
+ * the positions of helices based on secondary structure from a Stockholm file
+ *
+ * @param rnaAnnotation
+ */
+ private void _updateRnaSecStr(CharSequence rnaAnnotation)
+ {
+ try
+ {
+ _rnasecstr = Rna.getHelixMap(rnaAnnotation);
+ invalidrnastruc = -1;
+ } catch (WUSSParseException px)
+ {
+ // DEBUG System.out.println(px);
+ invalidrnastruc = px.getProblemPos();
+ }
+ if (invalidrnastruc > -1)
+ {
+ return;
+ }
+
+ if (_rnasecstr != null && _rnasecstr.length > 0)
+ {
+ // show all the RNA secondary structure annotation symbols.
+ isrna = true;
+ showAllColLabels = true;
+ scaleColLabel = true;
+ _markRnaHelices();
+ }
+ // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+
+ }
+
+ private void _markRnaHelices()
+ {
+ int mxval = 0;
+ // Figure out number of helices
+ // Length of rnasecstr is the number of pairs of positions that base pair
+ // with each other in the secondary structure
+ for (int x = 0; x < _rnasecstr.length; x++)
+ {
+
+ /*
+ * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+ * this.annotation._rnasecstr[x].getBegin());
+ */
+ // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+ int val = 0;
+ try
+ {
+ val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+ if (mxval < val)
+ {
+ mxval = val;
+ }
+ } catch (NumberFormatException q)
+ {
+ }
+ ;
+
+ annotations[_rnasecstr[x].getBegin()].value = val;
+ annotations[_rnasecstr[x].getEnd()].value = val;
+
+ // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+ // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+ }
+ setScore(mxval);
+ }
+
+ /**
* Checks if annotation labels represent secondary structures
*
*/
}
/**
- * Creates a new AlignmentAnnotation object.
- *
- * @param label
- * DOCUMENT ME!
- * @param description
- * DOCUMENT ME!
- * @param annotations
- * DOCUMENT ME!
- * @param min
- * DOCUMENT ME!
- * @param max
- * DOCUMENT ME!
- * @param winLength
- * DOCUMENT ME!
- */
- public AlignmentAnnotation(String label, String description,
- Annotation[] annotations, float min, float max, int graphType)
- {
- setAnnotationId();
- // graphs are not editable
- editable = graphType == 0;
-
- this.label = label;
- this.description = description;
- this.annotations = annotations;
- graph = graphType;
- graphMin = min;
- graphMax = max;
- validateRangeAndDisplay();
- }
-
- /**
* checks graphMin and graphMax, secondary structure symbols, sets graphType
* appropriately, sets null labels to the empty string if appropriate.
*/
}
/**
- * Copy constructor creates a new independent annotation row with the same
- * associated sequenceRef
- *
- * @param annotation
- */
- public AlignmentAnnotation(AlignmentAnnotation annotation)
- {
- setAnnotationId();
- this.label = new String(annotation.label);
- if (annotation.description != null)
- {
- this.description = new String(annotation.description);
- }
- this.graphMin = annotation.graphMin;
- this.graphMax = annotation.graphMax;
- this.graph = annotation.graph;
- this.graphHeight = annotation.graphHeight;
- this.graphGroup = annotation.graphGroup;
- this.groupRef = annotation.groupRef;
- this.editable = annotation.editable;
- this.autoCalculated = annotation.autoCalculated;
- this.hasIcons = annotation.hasIcons;
- this.hasText = annotation.hasText;
- this.height = annotation.height;
- this.label = annotation.label;
- this.padGaps = annotation.padGaps;
- this.visible = annotation.visible;
- this.centreColLabels = annotation.centreColLabels;
- this.scaleColLabel = annotation.scaleColLabel;
- this.showAllColLabels = annotation.showAllColLabels;
- this.calcId = annotation.calcId;
- if (annotation.properties != null)
- {
- properties = new HashMap<>();
- for (Map.Entry<String, String> val : annotation.properties.entrySet())
- {
- properties.put(val.getKey(), val.getValue());
- }
- }
- if (this.hasScore = annotation.hasScore)
- {
- this.score = annotation.score;
- }
- if (annotation.threshold != null)
- {
- threshold = new GraphLine(annotation.threshold);
- }
- Annotation[] ann = annotation.annotations;
- if (annotation.annotations != null)
- {
- this.annotations = new Annotation[ann.length];
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] != null)
- {
- annotations[i] = new Annotation(ann[i]);
- if (_linecolour != null)
- {
- _linecolour = annotations[i].colour;
- }
- }
- }
- }
- if (annotation.sequenceRef != null)
- {
- this.sequenceRef = annotation.sequenceRef;
- if (annotation.sequenceMapping != null)
- {
- Integer p = null;
- sequenceMapping = new HashMap<>();
- Iterator<Integer> pos = annotation.sequenceMapping.keySet()
- .iterator();
- while (pos.hasNext())
- {
- // could optimise this!
- p = pos.next();
- Annotation a = annotation.sequenceMapping.get(p);
- if (a == null)
- {
- continue;
- }
- if (ann != null)
- {
- for (int i = 0; i < ann.length; i++)
- {
- if (ann[i] == a)
- {
- sequenceMapping.put(p, annotations[i]);
- }
- }
- }
- }
- }
- else
- {
- this.sequenceMapping = null;
- }
- }
- // TODO: check if we need to do this: JAL-952
- // if (this.isrna=annotation.isrna)
- {
- // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
- }
- validateRangeAndDisplay(); // construct hashcodes, etc.
- }
-
- /**
* clip the annotation to the columns given by startRes and endRes (inclusive)
* and prune any existing sequenceMapping to just those columns.
*
return hasScore || !Double.isNaN(score);
}
- /**
- * Score only annotation
- *
- * @param label
- * @param description
- * @param score
- */
- public AlignmentAnnotation(String label, String description, double score)
- {
- this(label, description, null);
- setScore(score);
- }
-
- /**
- * copy constructor with edit based on the hidden columns marked in colSel
- *
- * @param alignmentAnnotation
- * @param colSel
- */
- public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
- HiddenColumns hidden)
- {
- this(alignmentAnnotation);
- if (annotations == null)
- {
- return;
- }
- makeVisibleAnnotation(hidden);
- }
-
public void setPadGaps(boolean padgaps, char gapchar)
{
this.padGaps = padgaps;
/**
* machine readable ID string indicating what generated this annotation
*/
- protected String calcId = "";
+ private String calcId = "";
/**
* properties associated with the calcId
Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
String label)
{
-
- ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+ List<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : list)
{
if ((calcId == null || (ann.getCalcId() != null
public static Iterable<AlignmentAnnotation> findAnnotation(
List<AlignmentAnnotation> list, String calcId)
{
-
List<AlignmentAnnotation> aa = new ArrayList<>();
if (calcId == null)
{
public void setHiddenColumns(HiddenColumns cols);
/**
+ * Insert a sequence at a position in an alignment
+ *
+ * @param i
+ * The index of the position.
+ * @param snew
+ * The new sequence.
+ */
+ void insertSequenceAt(int i, SequenceI snew);
+
+ /**
* Set the first sequence as representative and hide its insertions. Typically
* used when loading JPred files.
*/
*/
public HiddenColumns propagateInsertions(SequenceI profileseq,
AlignmentView input);
-
}
*/
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;
+
+/**
+ * stores data for each node in the hmm model
+ * @author TZVanaalten
+ *
+ */
+public class HMMNode
+{
+ //contains the match emissions for each symbol
+ double[] matchEmissions;
+
+ //contains the insert emissions for each symbol
+ double[] insertEmissions;
+
+ // contains the state transitions for each possible transition. These are mm,
+ // mi, md, im, ii, dm and dd in order
+ double[] stateTransitions;
+
+ //annotations
+ Integer alignmentColumn = null;
+ char consensusResidue;
+ char referenceAnnotation;
+ char maskValue;
+ char consensusStructure;
+
+ /**
+ * Constructor
+ */
+ public HMMNode()
+ {
+ }
+
+ public double[] getMatchEmissions()
+ {
+ return matchEmissions;
+ }
+
+ public double getMatchEmission(int symbolIndex)
+ {
+ return matchEmissions[symbolIndex];
+ }
+
+ public void setMatchEmissions(double[] matches)
+ {
+ this.matchEmissions = matches;
+ }
+
+ public double[] getInsertEmissions()
+ {
+ return insertEmissions;
+ }
+
+ public double getInsertEmission(int symbolIndex)
+ {
+ return insertEmissions[symbolIndex];
+ }
+
+ public void setInsertEmissions(double[] insertEmissionsL)
+ {
+ this.insertEmissions = insertEmissionsL;
+ }
+
+ public double[] getStateTransitions()
+ {
+ return stateTransitions;
+ }
+
+ public double getStateTransition(int transition)
+ {
+ return stateTransitions[transition];
+ }
+
+ public void setStateTransitions(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 jalview.io.HMMFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Data structure which stores a hidden Markov model
+ *
+ * @author TZVanaalten
+ *
+ */
+public class HiddenMarkovModel
+{
+ public final static String YES = "yes";
+
+ public final static String NO = "no";
+
+ 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;
+
+ private static final double LOG2 = Math.log(2);
+
+ /*
+ * properties read from HMM file header lines
+ */
+ Map<String, String> fileProperties = new HashMap<>();
+
+ String fileHeader;
+
+ /*
+ * the symbols used in this model e.g. "ACGT"
+ */
+ String alphabet;
+
+ /*
+ * symbol lookup index into the alphabet for 'A' to 'Z'
+ */
+ int[] symbolIndexLookup = new int['Z' - 'A' + 1];
+
+ /*
+ * Nodes in the model. The begin node is at index 0, and contains
+ * average emission probabilities for each symbol.
+ */
+ List<HMMNode> nodes = new ArrayList<>();
+
+ /*
+ * lookup of the HMM node for each alignment column (from 0)
+ */
+ Map<Integer, HMMNode> nodeLookup = new HashMap<>();
+
+ /**
+ * Constructor
+ */
+ public HiddenMarkovModel()
+ {
+ }
+
+ public HiddenMarkovModel(HiddenMarkovModel hmm)
+ {
+ super();
+ this.fileProperties = new HashMap<>(hmm.fileProperties);
+ this.alphabet = hmm.alphabet;
+ this.nodes = new ArrayList<>(hmm.nodes);
+ this.nodeLookup = new HashMap<>(hmm.nodeLookup);
+ this.symbolIndexLookup = hmm.symbolIndexLookup;
+ this.fileHeader = new String(hmm.fileHeader);
+ }
+
+ /**
+ * Returns the information content at a specified column, calculated as the
+ * sum (over possible symbols) of the log ratio
+ *
+ * <pre>
+ * log(emission probability / background probability) / log(2)
+ * </pre>
+ *
+ * @param column
+ * column position (base 0)
+ * @return
+ */
+ public float getInformationContent(int column)
+ {
+ float informationContent = 0f;
+
+ for (char symbol : getSymbols().toCharArray())
+ {
+ float freq = ResidueProperties.backgroundFrequencies
+ .get(getAlphabetType()).get(symbol);
+ float prob = (float) getMatchEmissionProbability(column, symbol);
+ informationContent += prob * Math.log(prob / freq);
+ }
+
+ informationContent = informationContent / (float) LOG2;
+
+ return informationContent;
+ }
+
+ /**
+ * 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 symbols used in this hidden Markov model
+ *
+ * @return
+ */
+ public String getSymbols()
+ {
+ return alphabet;
+ }
+
+ /**
+ * 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 nodes.get(nodeIndex);
+ }
+
+ /**
+ * Returns the name of the sequence alignment on which the HMM is based.
+ *
+ * @return
+ */
+ public String getName()
+ {
+ return fileProperties.get(HMMFile.NAME);
+ }
+
+ /**
+ * Answers the string value of the property (parsed from an HMM file) for the
+ * given key, or null if the property is not present
+ *
+ * @param key
+ * @return
+ */
+ public String getProperty(String key)
+ {
+ return fileProperties.get(key);
+ }
+
+ /**
+ * Answers true if the property with the given key is present with a value of
+ * "yes" (not case-sensitive), else false
+ *
+ * @param key
+ * @return
+ */
+ public boolean getBooleanProperty(String key)
+ {
+ return YES.equalsIgnoreCase(fileProperties.get(key));
+ }
+
+ /**
+ * Returns the length of the hidden Markov model, or 0 if not known
+ *
+ * @return
+ */
+ public int getLength()
+ {
+ if (fileProperties.get(HMMFile.LENGTH) == null)
+ {
+ return 0;
+ }
+ return Integer.parseInt(fileProperties.get(HMMFile.LENGTH));
+ }
+
+ /**
+ * Returns the value of mandatory property "ALPH" - "amino", "DNA", "RNA" are
+ * the options. Other alphabets may be added.
+ *
+ * @return
+ */
+ public String getAlphabetType()
+ {
+ return fileProperties.get(HMMFile.ALPHABET);
+ }
+
+ /**
+ * Sets the model alphabet to the symbols in the given string (ignoring any
+ * whitespace), and returns the number of symbols
+ *
+ * @param symbols
+ */
+ public int setAlphabet(String symbols)
+ {
+ String trimmed = symbols.toUpperCase().replaceAll("\\s", "");
+ int count = trimmed.length();
+ alphabet = trimmed;
+ symbolIndexLookup = new int['Z' - 'A' + 1];
+ Arrays.fill(symbolIndexLookup, -1);
+ int ignored = 0;
+
+ /*
+ * save the symbols in order, and a quick lookup of symbol position
+ */
+ for (short i = 0; i < count; i++)
+ {
+ char symbol = trimmed.charAt(i);
+ if (symbol >= 'A' && symbol <= 'Z'
+ && symbolIndexLookup[symbol - 'A'] == -1)
+ {
+ symbolIndexLookup[symbol - 'A'] = i;
+ }
+ else
+ {
+ System.err
+ .println(
+ "Unexpected or duplicated character in HMM ALPHabet: "
+ + symbol);
+ ignored++;
+ }
+ }
+ return count - ignored;
+ }
+
+ /**
+ * 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 = getSymbolIndex(symbol);
+ double probability = 0d;
+ if (symbolIndex != -1 && nodeLookup.containsKey(alignColumn))
+ {
+ HMMNode node = nodeLookup.get(alignColumn);
+ probability = node.getMatchEmission(symbolIndex);
+ }
+ return probability;
+ }
+
+ /**
+ * 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 = getSymbolIndex(symbol);
+ double probability = 0d;
+ if (symbolIndex != -1 && nodeLookup.containsKey(alignColumn))
+ {
+ HMMNode node = nodeLookup.get(alignColumn);
+ probability = node.getInsertEmission(symbolIndex);
+ }
+ return probability;
+ }
+
+ /**
+ * 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)
+ {
+ double probability = 0d;
+ if (nodeLookup.containsKey(alignColumn))
+ {
+ HMMNode node = nodeLookup.get(alignColumn);
+ probability = node.getStateTransition(transition);
+ }
+ return probability;
+ }
+
+ /**
+ * 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 (getBooleanProperty(HMMFile.CONSENSUS_RESIDUE))
+ {
+ HMMNode node = nodeLookup.get(columnIndex);
+ if (node == null)
+ {
+ return '-';
+ }
+ mostLikely = node.getConsensusResidue();
+ return mostLikely;
+ }
+ else
+ {
+ double highestProb = 0;
+ for (char character : alphabet.toCharArray())
+ {
+ 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 number of symbols in the alphabet used in this HMM.
+ *
+ * @return
+ */
+ public int getNumberOfSymbols()
+ {
+ return alphabet.length();
+ }
+
+ /**
+ * Sets a property read from an HMM file
+ *
+ * @param key
+ * @param value
+ */
+ public void setProperty(String key, String value)
+ {
+ fileProperties.put(key, value);
+ }
+
+ /**
+ * Sets the alignment column of the specified node
+ *
+ * @param nodeIndex
+ *
+ * @param column
+ *
+ */
+ public void setAlignmentColumn(HMMNode node, int column)
+ {
+ node.setAlignmentColumn(column);
+ nodeLookup.put(column, node);
+ }
+
+ /**
+ * Updates the mapping of nodes of the HMM to non-gapped positions of the
+ * sequence. Nodes 1, 2, 3... are mapped to the columns occupied by the first,
+ * second, third... residues of the sequence. The 'begin' node (node 0) of the
+ * HMM is not mapped.
+ *
+ * @param sequence
+ */
+ public void updateMapping(char[] sequence)
+ {
+ int nodeNo = 1;
+ int column = 0;
+ synchronized (nodeLookup)
+ {
+ clearNodeLookup();
+ for (char residue : sequence)
+ {
+ if (!Comparison.isGap(residue))
+ {
+ HMMNode node = nodes.get(nodeNo);
+ if (node == null)
+ {
+ // error : too few nodes for sequence
+ break;
+ }
+ setAlignmentColumn(node, column);
+ nodeNo++;
+ }
+ column++;
+ }
+ }
+ }
+
+ /**
+ * Clears all data in the node lookup map
+ */
+ public void clearNodeLookup()
+ {
+ nodeLookup.clear();
+ }
+
+ /**
+ * 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 getViterbi()
+ {
+ String value;
+ value = fileProperties.get(HMMFile.VITERBI);
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getMSV()
+ {
+ String value;
+ value = fileProperties.get(HMMFile.MSV);
+ return value;
+ }
+
+ /**
+ * Temporary implementation, should not be used.
+ *
+ * @return
+ */
+ public String getForward()
+ {
+ String value;
+ value = fileProperties.get(HMMFile.FORWARD);
+ return value;
+ }
+
+ /**
+ * Answers the HMMNode mapped to the given alignment column (base 0), or null
+ * if none is mapped
+ *
+ * @param alignmentColumn
+ */
+ public HMMNode getNodeForColumn(int alignmentColumn)
+ {
+ return nodeLookup.get(alignmentColumn);
+ }
+
+ /**
+ * 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.
+ *
+ * @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(), 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;
+ }
+
+ /**
+ * Answers the index position (0...) of the given symbol, or -1 if not a valid
+ * symbol for this HMM
+ *
+ * @param symbol
+ * @return
+ */
+ public int getSymbolIndex(char symbol)
+ {
+ /*
+ * symbolIndexLookup holds the index for 'A' to 'Z'
+ */
+ char c = Character.toUpperCase(symbol);
+ if ('A' <= c && c <= 'Z')
+ {
+ return symbolIndexLookup[c - 'A'];
+ }
+ return -1;
+ }
+
+ public void addNode(HMMNode node)
+ {
+ nodes.add(node);
+ }
+}
+
import jalview.util.QuickSort;
import jalview.util.SparseCount;
+import java.util.List;
+
/**
* A class to count occurrences of residues in a profile, optimised for speed
* and memory footprint.
}
/**
+ * A constructor that counts frequency of all symbols (including gaps) in the
+ * sequences (not case-sensitive)
+ *
+ * @param sequences
+ */
+ public ResidueCount(List<SequenceI> sequences)
+ {
+ this();
+ for (SequenceI seq : sequences)
+ {
+ for (int i = 0; i < seq.getLength(); i++)
+ {
+ add(seq.getCharAt(i));
+ }
+ }
+ }
+
+ /**
* Increments the count for the given character. The supplied character may be
* upper or lower case but counts are for the upper case only. Gap characters
* (space, ., -) are all counted together.
sb.append("]");
return sb.toString();
}
+
+ /**
+ * Answers the total count for all symbols (excluding gaps)
+ *
+ * @return
+ */
+ public int getTotalResidueCount()
+ {
+ int total = 0;
+ for (char symbol : this.getSymbolCounts().symbols)
+ {
+ total += getCount(symbol);
+ }
+ return total;
+ }
}
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
+import jalview.workers.InformationThread;
import java.util.ArrayList;
import java.util.Arrays;
int end;
+ HiddenMarkovModel hmm;
+
+ boolean isHMMConsensusSequence = false;
+
Vector<PDBEntry> pdbIds;
String vamsasId;
this.addPDBId(new PDBEntry(pdb));
}
}
+ if (seq.isHMMConsensusSequence())
+ {
+ this.isHMMConsensusSequence = true;
+ }
+ if (seq.getHMM() != null)
+ {
+ this.hmm = new HiddenMarkovModel(seq.getHMM());
+ }
+
}
@Override
@Override
public Vector<PDBEntry> getAllPDBEntries()
{
- return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
+ return pdbIds == null ? new Vector<>() : pdbIds;
}
/**
{
for (AlignmentAnnotation ann : annotation)
{
- if (ann.calcId != null && ann.calcId.equals(calcId)
+ String id = ann.getCalcId();
+ if (id != null && id.equals(calcId)
&& ann.label != null && ann.label.equals(label))
{
result.add(ann);
}
}
+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel hmm)
+ {
+ this.hmm = hmm;
+ }
+
+ @Override
+ public void updateHMMMapping()
+ {
+ if (hmm == null)
+ {
+ return;
+ }
+ hmm.updateMapping(sequence);
+ }
+
+ /**
+ * Maps the HMM sequence to the reference annotation.
+ *
+ * @param rf
+ */
+ @Override
+ public void mapToReference(AlignmentAnnotation rf)
+ {
+ if (this.isHMMConsensusSequence)
+ {
+ int node = 1;
+ hmm.clearNodeLookup();
+ for (int i = 0; i < getLength(); i++)
+ {
+ if (rf.annotations[i].displayCharacter.equalsIgnoreCase("x"))
+ {
+ if (i < hmm.getNodeAlignmentColumn(node))
+ {
+ this.deleteChars(i, hmm.getNodeAlignmentColumn(node));
+ updateHMMMapping();
+ }
+ else if (i > hmm.getNodeAlignmentColumn(node))
+ {
+ int length = i - hmm.getNodeAlignmentColumn(node);
+ this.insertCharAt(hmm.getNodeAlignmentColumn(node), length,
+ '-');
+ updateHMMMapping();
+ }
+ node++;
+ }
+ }
+ }
+ }
+
+ @Override
+ public boolean isHMMConsensusSequence()
+ {
+ return isHMMConsensusSequence;
+ }
+
+ @Override
+ public void setIsHMMConsensusSequence(boolean value)
+ {
+ this.isHMMConsensusSequence = value;
+ }
+
+ @Override
+ public boolean hasHMMAnnotation()
+ {
+ if (this.annotation == null) {
+ return false;
+ }
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
/**
* {@inheritDoc}
*/
* @return
*/
boolean isNucleotide();
+
+ /**
+ * Returns the HMM consensus sequence (if any) for the collection, or null
+ *
+ * @return
+ */
+ SequenceI getHmmConsensus();
+
+ /**
+ * Sets the HMM consensus sequence for the collection
+ */
+ void setHmmConsensus(SequenceI hmmSeq);
}
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+import jalview.workers.InformationThread;
import java.awt.Color;
import java.beans.PropertyChangeListener;
public class SequenceGroup implements AnnotatedCollectionI
{
// TODO ideally this event notification functionality should be separated into
- // a
- // subclass of ViewportProperties similarly to ViewportRanges. Done here as
- // quick fix for JAL-2665
+ // a subclass of ViewportProperties similarly to ViewportRanges.
+ // Done here as a quick fix for JAL-2665
public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
- protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
+ private String groupName;
- public void addPropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
+ private String description;
- public void removePropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(listener);
- }
- // end of event notification functionality initialisation
+ private AnnotatedCollectionI context;
- String groupName;
+ private Conservation conservationData;
- String description;
+ private ProfilesI consensusProfiles;
- Conservation conserve;
+ private ProfilesI hmmProfiles;
- boolean displayBoxes = true;
+ private boolean displayBoxes = true;
- boolean displayText = true;
+ private boolean displayText = true;
- boolean colourText = false;
+ private boolean colourText = false;
- /**
- * True if the group is defined as a group on the alignment, false if it is
- * just a selection.
+ /*
+ * true if the group is defined as a group on the alignment, false if it is
+ * just a selection
*/
- boolean isDefined = false;
+ private boolean isDefined;
- /**
+ /*
* after Olivier's non-conserved only character display
*/
- boolean showNonconserved = false;
+ private boolean showNonconserved;
- /**
- * group members
+ /*
+ * sequences in the group
*/
private List<SequenceI> sequences = new ArrayList<>();
- /**
+ /*
* representative sequence for this group (if any)
*/
- private SequenceI seqrep = null;
+ private SequenceI seqrep;
+
+ /*
+ * HMM consensus sequence for group (if any)
+ */
+ private SequenceI hmmConsensus;
- int width = -1;
+ private int width = -1;
- /**
- * Colourscheme applied to group if any
+ /*
+ * colour scheme applied to group if any
*/
public ResidueShaderI cs;
// start column (base 0)
- int startRes = 0;
+ private int startRes;
// end column (base 0)
- int endRes = 0;
+ private int endRes;
public Color outlineColour = Color.black;
- public Color idColour = null;
+ public Color idColour;
- public int thresholdTextColour = 0;
+ public int thresholdTextColour;
public Color textColour = Color.black;
public Color textColour2 = Color.white;
- /**
- * consensus calculation property
+ /*
+ * properties for consensus annotation
*/
private boolean ignoreGapsInConsensus = true;
- /**
- * consensus calculation property
- */
- private boolean showSequenceLogo = false;
+ private boolean showSequenceLogo;
- /**
- * flag indicating if logo should be rendered normalised
- */
private boolean normaliseSequenceLogo;
+ private boolean showConsensusHistogram;
+
+ /*
+ * properties for HMM information annotation
+ */
+ private boolean hmmIgnoreBelowBackground = true;
+
+ private boolean hmmUseInfoLetterHeight;
+
+ private boolean showHMMSequenceLogo;
+
+ private boolean hmmNormaliseSequenceLogo;
+
+ private boolean hmmShowHistogram;
+
/*
* visibility of rows or represented rows covered by group
*/
- private boolean hidereps = false;
+ private boolean hidereps;
/*
* visibility of columns intersecting this group
*/
- private boolean hidecols = false;
-
- AlignmentAnnotation consensus = null;
+ private boolean hidecols;
- AlignmentAnnotation conservation = null;
+ private AlignmentAnnotation consensus;
- private boolean showConsensusHistogram;
+ private AlignmentAnnotation conservation;
- private AnnotatedCollectionI context;
+ private AlignmentAnnotation hmmInformation;
/**
- * Creates a new SequenceGroup object.
+ * Constructor, assigning a generated default name of "JGroup:" with object
+ * hashcode appended
*/
public SequenceGroup()
{
showSequenceLogo = seqsel.showSequenceLogo;
normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
showConsensusHistogram = seqsel.showConsensusHistogram;
+ showHMMSequenceLogo = seqsel.showHMMSequenceLogo;
+ hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
+ hmmShowHistogram = seqsel.hmmShowHistogram;
idColour = seqsel.idColour;
outlineColour = seqsel.outlineColour;
seqrep = seqsel.seqrep;
thresholdTextColour = seqsel.thresholdTextColour;
width = seqsel.width;
ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
- if (seqsel.conserve != null)
+ hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground;
+ hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight;
+ if (seqsel.conservationData != null)
{
recalcConservation(); // safer than
// aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
}
}
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
+ public void addPropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ public void removePropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
seqs[ipos].setDescription(seq.getDescription());
seqs[ipos].setDBRefs(seq.getDBRefs());
seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+ seqs[ipos].setIsHMMConsensusSequence(seq.isHMMConsensusSequence());
if (seq.getDatasetSequence() != null)
{
seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
*/
public Conservation getConservation()
{
- return conserve;
+ return conservationData;
}
/**
*/
public void setConservation(Conservation c)
{
- conserve = c;
+ conservationData = c;
}
/**
*/
public boolean recalcConservation()
{
- return recalcConservation(false);
+ return recalcAnnotations(false);
}
/**
- * calculate residue conservation for group - but only if necessary. returns
- * true if the calculation resulted in a visible change to group
+ * Recalculates column consensus, conservation, and HMM annotation for the
+ * group (as applicable). Returns true if the calculation resulted in a
+ * visible change to group.
*
* @param defer
* when set, colourschemes for this group are not refreshed after
* recalculation
*/
- public boolean recalcConservation(boolean defer)
+ public boolean recalcAnnotations(boolean defer)
{
- if (cs == null && consensus == null && conservation == null)
+ if (cs == null && consensus == null && conservation == null
+ && hmmInformation == null)
{
return false;
}
{
ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
endRes + 1, showSequenceLogo);
+ if (hmmInformation != null)
+ {
+ HiddenMarkovModel hmm = hmmInformation.sequenceRef.getHMM();
+
+ ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
+ (endRes + 1) - startRes, startRes, endRes + 1,
+ showHMMSequenceLogo, hmmIgnoreBelowBackground,
+ hmmUseInfoLetterHeight);
+ _updateInformationRow(info, sequences.size());
+ upd = true;
+ }
if (consensus != null)
{
_updateConsensusRow(cnsns, sequences.size());
c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
- public ProfilesI consensusData = null;
-
private void _updateConsensusRow(ProfilesI cnsns, long nseq)
{
if (consensus == null)
}
consensus.label = "Consensus for " + getName();
consensus.description = "Percent Identity";
- consensusData = cnsns;
+ consensusProfiles = cnsns;
// preserve width if already set
int aWidth = (consensus.annotations != null)
? (endRes < consensus.annotations.length
}
/**
+ * Recalculates the information content on the HMM annotation.
+ *
+ * @param cnsns
+ * @param nseq
+ */
+ private void _updateInformationRow(ProfilesI cnsns, long nseq)
+ {
+ if (hmmInformation == null)
+ {
+ createInformationAnnotation();
+ }
+ hmmInformation.description = MessageManager
+ .getString("label.information_description");
+ setHmmProfiles(cnsns);
+ // preserve width if already set
+ int aWidth = (hmmInformation.annotations != null)
+ ? (endRes < hmmInformation.annotations.length
+ ? hmmInformation.annotations.length : endRes + 1)
+ : endRes + 1;
+ hmmInformation.annotations = null;
+ hmmInformation.annotations = new Annotation[aWidth]; // should be alignment
+ // width
+ hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+ AAFrequency.completeInformation(hmmInformation, cnsns, startRes,
+ endRes + 1, nseq, 0f);
+ }
+
+ /**
* @param s
* sequence to either add or remove from group
* @param recalc
}
/**
+ * Creates the Hidden Markov Model annotation for this group
+ */
+ void createInformationAnnotation()
+ {
+ hmmInformation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+ 6.25f, AlignmentAnnotation.BAR_GRAPH);
+ hmmInformation.hasText = true;
+ hmmInformation.autoCalculated = false;
+ hmmInformation.groupRef = this;
+ hmmInformation.label = getName();
+ hmmInformation.description = MessageManager
+ .getString("label.information_description");
+ hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+ }
+
+ /**
* set this alignmentAnnotation object as the one used to render consensus
* annotation
*
ignoreGapsInConsensus = state;
}
- public boolean getIgnoreGapsConsensus()
+ public boolean isIgnoreGapsConsensus()
{
return ignoreGapsInConsensus;
}
+ public void setIgnoreBelowBackground(boolean state)
+ {
+ hmmIgnoreBelowBackground = state;
+ }
+
+ public boolean isIgnoreBelowBackground()
+ {
+ return hmmIgnoreBelowBackground;
+ }
+
+ public void setInfoLetterHeight(boolean state)
+ {
+ hmmUseInfoLetterHeight = state;
+ }
+
+ public boolean isUseInfoLetterHeight()
+ {
+ return hmmUseInfoLetterHeight;
+ }
+
/**
* @param showSequenceLogo
* indicates if a sequence logo is shown for consensus annotation
{
return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
}
+
+ public boolean isShowInformationHistogram()
+ {
+ return hmmShowHistogram;
+ }
+
+ public void setShowInformationHistogram(boolean state)
+ {
+ if (hmmShowHistogram != state && hmmInformation != null)
+ {
+ this.hmmShowHistogram = state;
+ // recalcConservation(); TODO don't know what to do here next
+ }
+ this.hmmShowHistogram = state;
+
+ }
+
+ public boolean isShowHMMSequenceLogo()
+ {
+ return showHMMSequenceLogo;
+ }
+
+ public void setshowHMMSequenceLogo(boolean state)
+ {
+ showHMMSequenceLogo = state;
+
+ }
+
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return hmmNormaliseSequenceLogo;
+ }
+
+ public void setNormaliseHMMSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+ @Override
+ public SequenceI getHmmConsensus()
+ {
+ return hmmConsensus;
+ }
+
+ @Override
+ public void setHmmConsensus(SequenceI hmmSeq)
+ {
+ this.hmmConsensus = hmmSeq;
+ }
+
+ public ProfilesI getConsensusData()
+ {
+ return consensusProfiles;
+ }
+
+ public ProfilesI getHmmProfiles()
+ {
+ return hmmProfiles;
+ }
+
+ public void setHmmProfiles(ProfilesI hmmProfiles)
+ {
+ this.hmmProfiles = hmmProfiles;
+ }
+
}
*/
public void setName(String name);
+ public HiddenMarkovModel getHMM();
+
+ public void setHMM(HiddenMarkovModel hmm);
+
/**
* Get the display name
*/
public List<DBRefEntry> getPrimaryDBRefs();
/**
+ * Updates mapping of Hidden Markov Model nodes to aligned sequence positions
+ * (e.g. after an alignment edit). The nodes of the HMM (excluding the first
+ * node, with model average values), are associated in turn with non-gapped
+ * sequence positions.
+ */
+ public void updateHMMMapping();
+
+ boolean isHMMConsensusSequence();
+
+ void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
+
+ /**
+ * Answers true if the sequence has annotation for Hidden Markov Model
+ * information content, else false
+ */
+ boolean hasHMMAnnotation();
+
+ /**
* Returns a (possibly empty) list of sequence features that overlap the given
* alignment column range, optionally restricted to one or more specified
* feature types. If the range is all gaps, then features which enclose it are
*/
BitSet getInsertionsAsBits();
+ void mapToReference(AlignmentAnnotation rf);
+
/**
* Replaces every occurrence of c1 in the sequence with c2 and returns the
* number of characters changed
* @param c1
* @param c2
*/
- public int replace(char c1, char c2);
+ int replace(char c1, char c2);
/**
* Answers the GeneLociI, or null if not known
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.HMMAlign;
+import jalview.hmmer.HMMBuild;
+import jalview.hmmer.HMMERParamStore;
+import jalview.hmmer.HMMERPreset;
+import jalview.hmmer.HMMSearch;
+import jalview.hmmer.HmmerCommand;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
+import jalview.util.StringUtils;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
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.Scanner;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
import javax.swing.JInternalFrame;
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;
AlignViewport viewport;
public AlignViewControllerI avc;
+ /*
+ * The selected HMM for this align frame
+ */
+ SequenceI selectedHMMSequence;
List<AlignmentPanel> alignPanels = new ArrayList<>();
*/
String fileName = null;
+
/**
* Creates a new AlignFrame object with specific width and height.
*
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 hmmBuildSettings_actionPerformed()
+ {
+ if (!(alignmentIsSufficient(1)))
+ {
+ return;
+ }
+ WsParamSetI set = new HMMERPreset();
+ List<ArgumentI> args = new ArrayList<>();
+ ParamDatastoreI store = new HMMERParamStore("hmmbuild");
+ WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
+ args);
+ if (params.showRunDialog())
+ {
+ new Thread(new HMMBuild(this, params.getJobParams())).start();
+ }
+ alignPanel.repaint();
+
+ }
+
+ @Override
+ public void hmmAlignSettings_actionPerformed()
+ {
+ if (!(checkForHMM() && alignmentIsSufficient(2)))
+ {
+ return;
+ }
+ WsParamSetI set = new HMMERPreset();
+ List<ArgumentI> args = new ArrayList<>();
+ ParamDatastoreI store = new HMMERParamStore("hmmalign");
+ WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
+ args);
+ if (params.showRunDialog())
+ {
+ new Thread(new HMMAlign(this, params.getJobParams()))
+ .start();
+ }
+ alignPanel.repaint();
+ }
+
+ @Override
+ public void hmmSearchSettings_actionPerformed()
+ {
+ if (!checkForHMM())
+ {
+ return;
+ }
+ WsParamSetI set = new HMMERPreset();
+ List<ArgumentI> args = new ArrayList<>();
+ ParamDatastoreI store = new HMMERParamStore("hmmsearch");
+ WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
+ args);
+ if (params.showRunDialog())
+ {
+ new Thread(new HMMSearch(this, params.getJobParams()))
+ .start();
+ }
+ alignPanel.repaint();
+ }
+
+ @Override
+ public void hmmBuildRun_actionPerformed()
+ {
+ if (!alignmentIsSufficient(1))
+ {
+ return;
+ }
+ new Thread(new HMMBuild(this, null))
+ .start();
+ }
+
+ @Override
+ public void hmmAlignRun_actionPerformed()
+ {
+ if (!(checkForHMM() && alignmentIsSufficient(2)))
+ {
+ return;
+ }
+ new Thread(new HMMAlign(this, null)).start();
+ }
+
+ @Override
+ public void hmmSearchRun_actionPerformed()
+ {
+ if (!checkForHMM())
+ {
+ return;
+ }
+ new Thread(new HMMSearch(this, null)).start();
+ }
+
+ /**
+ * Checks if the frame has a selected hidden Markov model
+ *
+ * @return
+ */
+ private boolean checkForHMM()
+ {
+ if (getSelectedHMM() == null)
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.no_selected_hmm"));
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Checks if the alignment contains the required number of sequences.
+ *
+ * @param required
+ * @return
+ */
+ public boolean alignmentIsSufficient(int required)
+ {
+ if (getViewport().getAlignment().getSequences().size() < required)
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.not_enough_sequences"));
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ public void addDatabase_actionPerformed() throws IOException
+ {
+ if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
+ {
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+ Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+ }
+
+ String path = openFileChooser(false);
+ if (new File(path).exists())
+ {
+ IdentifyFile identifier = new IdentifyFile();
+ FileFormatI format = identifier.identify(path, DataSourceType.FILE);
+ if (format == FileFormat.Fasta || format == FileFormat.Stockholm
+ || format == FileFormat.Pfam)
+ {
+ String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+ String currentDbPaths = Cache
+ .getProperty(Preferences.HMMSEARCH_DB_PATHS);
+ currentDbPaths += " " + path;
+
+ String fileName = StringUtils.getLastToken(path, File.separator);
+ Scanner scanner = new Scanner(fileName).useDelimiter(".");
+ String name = scanner.next();
+ scanner.close();
+ currentDbs += " " + path; // TODO remove path from file name
+ scanner.close();
+
+ Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
+ }
+ else
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.invalid_format"));
+ }
+ }
+ else
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.not_enough_sequences"));
+ }
+ }
+
+ /**
+ * Opens a file chooser
+ *
+ * @param forFolder
+ * @return
+ */
+ protected String openFileChooser(boolean forFolder)
+ {
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
+ @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(
*
* @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());
}
}
+ /**
+ * Sets the status of the HMMER menu
+ */
+ public void updateHMMERStatus()
+ {
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+ }
+
+ /**
+ * Returns the selected hidden Markov model.
+ *
+ * @return
+ */
+ public HiddenMarkovModel getSelectedHMM()
+ {
+ if (selectedHMMSequence == null)
+ {
+ return null;
+ }
+ return selectedHMMSequence.getHMM();
+ }
+
+ /**
+ * Returns the selected hidden Markov model.
+ *
+ * @return
+ */
+ public SequenceI getSelectedHMMSequence()
+ {
+ return selectedHMMSequence;
+ }
+
+ /**
+ * Sets the selected hidden Markov model
+ *
+ * @param selectedHMM
+ */
+ public void setSelectedHMMSequence(SequenceI selectedHMM)
+ {
+ this.selectedHMMSequence = selectedHMM;
+ hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
+ + selectedHMM.getHMM().getName());
+ hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
+ + selectedHMM.getHMM().getName());
+ }
+
+ @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");
+ }
+ }
+
@Override
protected void loadVcf_actionPerformed()
{
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
+import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
+import java.util.Vector;
import javax.swing.JInternalFrame;
private AnnotationColumnChooser annotationColumnSelectionState;
+ boolean validCharWidth;
+
+ public boolean followSelection = true;
+
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
+
/**
* Creates a new AlignViewport object.
*
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
- alignment
- .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ AlignmentI al = getAlignment();
+ al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
- if (hconsensus == null && !isDataset)
+ if (consensusProfiles == null && !isDataset)
{
- if (!alignment.isNucleotide())
+ if (!al.isNucleotide())
{
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
showQuality = Cache.getDefault("SHOW_QUALITY", true);
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
- String colourProperty = alignment.isNucleotide()
+ // initInformation();
+
+ String colourProperty = al.isNucleotide()
? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
ResidueColourScheme.NONE);
}
ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(alignment, schemeName);
+ .getColourScheme(al, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(consensusProfiles);
}
}
- boolean validCharWidth;
-
/**
* {@inheritDoc}
*/
/*
* replace mappings on our alignment
*/
- if (alignment != null && align != null)
+ if (getAlignment() != null && align != null)
{
- alignment.setCodonFrames(align.getCodonFrames());
+ getAlignment().setCodonFrames(align.getCodonFrames());
}
}
}
/**
- * returns the visible column regions of the alignment
+ * Returns an iterator over the visible column regions of the alignment
*
* @param selectedRegionOnly
* true to just return the contigs intersecting with the selected
}
else
{
- end = alignment.getWidth();
+ end = getAlignment().getWidth();
}
- return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
- false));
+
+ return getAlignment().getHiddenColumns().getVisContigsIterator(start,
+ end, false);
}
/**
return false;
}
- public boolean followSelection = true;
-
/**
* @return true if view selection should always follow the selections
* broadcast by other selection sources
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<>();
-
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
return calcIdParams.get(calcId);
}
fr.setTransparency(featureSettings.getTransparency());
}
+
+ @Override
+ public boolean isNormaliseHMMSequenceLogo()
+ {
+ return normaliseHMMSequenceLogo;
+ }
+
}
import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.workers.InformationThread;
import java.awt.Color;
import java.awt.Cursor;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
pop.show(this, evt.getX(), evt.getY());
return;
}
+
+ final AlignmentAnnotation ann = aa[selectedRow];
+ final boolean isSequenceAnnotation = ann.sequenceRef != null;
+
item = new JMenuItem(EDITNAME);
item.addActionListener(this);
pop.add(item);
// JAL-1264 hide all sequence-specific annotations of this type
if (selectedRow < aa.length)
{
- if (aa[selectedRow].sequenceRef != null)
+ if (isSequenceAnnotation)
{
- final String label = aa[selectedRow].label;
+ final String label = ann.label;
JMenuItem hideType = new JMenuItem();
String text = MessageManager.getString("label.hide_all") + " "
+ label;
AlignmentUtils.showOrHideSequenceAnnotations(
ap.av.getAlignment(), Collections.singleton(label),
null, false, false);
- // for (AlignmentAnnotation ann : ap.av.getAlignment()
- // .getAlignmentAnnotation())
- // {
- // if (ann.sequenceRef != null && ann.label != null
- // && ann.label.equals(label))
- // {
- // ann.visible = false;
- // }
- // }
ap.refresh(true);
}
});
// property methods
if (selectedRow < aa.length)
{
- final String label = aa[selectedRow].label;
- if (!aa[selectedRow].autoCalculated)
+ final String label = ann.label;
+ if (!(ann.autoCalculated)
+ && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId())))
{
- if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+ if (ann.graph == AlignmentAnnotation.NO_GRAPH)
{
// display formatting settings for this row.
pop.addSeparator();
// av and sequencegroup need to implement same interface for
item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
- aa[selectedRow].scaleColLabel);
+ ann.scaleColLabel);
item.addActionListener(this);
pop.add(item);
}
}
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)
- ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
- : ap.av.isIgnoreGapsConsensus());
- final AlignmentAnnotation aaa = aa[selectedRow];
- cbmi.addActionListener(new ActionListener()
+ addConsensusMenu(pop, ann);
+ }
+ else if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ addHmmerMenu(pop, ann);
+ }
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ /**
+ * Adds context menu options for (alignment or group) Hmmer annotation
+ *
+ * @param pop
+ * @param ann
+ */
+ protected void addHmmerMenu(JPopupMenu pop, final AlignmentAnnotation ann)
+ {
+ final boolean isGroupAnnotation = ann.groupRef != null;
+ pop.addSeparator();
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString(
+ "label.ignore_below_background_frequency"),
+ isGroupAnnotation
+ ? ann.groupRef
+ .isIgnoreBelowBackground()
+ : ap.av.isIgnoreBelowBackground());
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
{
- @Override
- public void actionPerformed(ActionEvent e)
+ if (!ann.groupRef.isUseInfoLetterHeight())
{
- if (aaa.groupRef != null)
- {
- // TODO: pass on reference to ap so the view can be updated.
- aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.getAnnotationPanel()
- .paint(ap.getAnnotationPanel().getGraphics());
- }
- else
- {
- ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
- }
- ap.alignmentChanged();
+ ann.groupRef.setIgnoreBelowBackground(cbmi.getState());
}
- });
- pop.add(cbmi);
- // av and sequencegroup need to implement same interface for
- if (aaa.groupRef != null)
+ }
+ else if (!ap.av.isInfoLetterHeight())
{
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_group_histogram"),
- aa[selectedRow].groupRef.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setShowConsensusHistogram(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.isShowSequenceLogo());
- cprofl.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setshowSequenceLogo(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.isNormaliseSequenceLogo());
- cproflnorm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
+ ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(cbmi);
+ final JCheckBoxMenuItem letterHeight = new JCheckBoxMenuItem(
+ MessageManager.getString("label.use_info_for_height"),
+ isGroupAnnotation ? ann.groupRef.isUseInfoLetterHeight()
+ : ap.av.isInfoLetterHeight());
+ letterHeight.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
+ {
+ ann.groupRef.setInfoLetterHeight((letterHeight.getState()));
+ ann.groupRef.setIgnoreBelowBackground(true);
+ }
+ else
+ {
+ ap.av.setInfoLetterHeight(letterHeight.getState(), ap);
+ ap.av.setIgnoreBelowBackground(true, ap);
+ }
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(letterHeight);
+ if (isGroupAnnotation)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ ann.groupRef.isShowInformationHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ ann.groupRef.isShowHMMSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setshowHMMSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ ann.groupRef.isNormaliseHMMSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef
+ .setNormaliseHMMSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ ann.groupRef.setshowHMMSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ 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)
+ {
+ av.setShowInformationHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ 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)
+ {
+ av.updateInformation(ap);
+ av.setShowHMMSequenceLogo(cprof.getState());
+ ap.repaint();
+ }
+ });
+ 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)
+ {
+ av.setShowHMMSequenceLogo(true);
+ av.setNormaliseHMMSequenceLogo(cprofnorm.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ }
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
- // automatically enable logo display if we're clicked
- aaa.groupRef.setshowSequenceLogo(true);
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cproflnorm);
+ /**
+ * Adds context menu options for (alignment or group) Consensus annotation
+ *
+ * @param pop
+ * @param ann
+ */
+ protected void addConsensusMenu(JPopupMenu pop,
+ final AlignmentAnnotation ann)
+ {
+ final boolean isGroupAnnotation = ann.groupRef != null;
+ pop.addSeparator();
+
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ MessageManager.getString("label.ignore_gaps_consensus"),
+ (ann.groupRef != null)
+ ? ann.groupRef.isIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
+ cbmi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (isGroupAnnotation)
+ {
+ ann.groupRef.setIgnoreGapsConsensus(cbmi.getState());
}
else
{
- final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_histogram"),
- av.isShowConsensusHistogram());
- chist.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowConsensusHistogram(chist.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(chist);
- final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
- MessageManager.getString("label.show_logo"),
- av.isShowSequenceLogo());
- cprof.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(cprof.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cprof);
- final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
- MessageManager.getString("label.normalise_logo"),
- av.isNormaliseSequenceLogo());
- cprofnorm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- // TODO: pass on reference
- // to ap
- // so the
- // view
- // can be
- // updated.
- av.setShowSequenceLogo(true);
- av.setNormaliseSequenceLogo(cprofnorm.getState());
- ap.alignFrame.setMenusForViewport();
- ap.repaint();
- // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
- }
- });
- pop.add(cprofnorm);
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
- final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
- consclipbrd.addActionListener(this);
- pop.add(consclipbrd);
+ ap.alignmentChanged();
}
+ });
+ pop.add(cbmi);
+ if (isGroupAnnotation)
+ {
+ /*
+ * group consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_histogram"),
+ ann.groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_group_logo"),
+ ann.groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ ann.groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ann.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ ann.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ }
+ });
+ pop.add(cproflnorm);
}
- pop.show(this, evt.getX(), evt.getY());
+ else
+ {
+ /*
+ * alignment consensus options
+ */
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_histogram"),
+ av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ MessageManager.getString("label.show_logo"),
+ av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowSequenceLogo(cprof.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ MessageManager.getString("label.normalise_logo"),
+ av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.setShowSequenceLogo(true);
+ av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.repaint();
+ }
+ });
+ pop.add(cprofnorm);
+ }
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
}
/**
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
-
}
}
return;
@Override
public void paintComponent(Graphics g)
{
-
int width = getWidth();
if (width == 0)
{
}
drawComponent(g2, true, width);
-
}
/**
*/
final String name = scheme.getSchemeName();
String label = MessageManager.getStringOrReturn(
- "label.colourScheme_" + name.toLowerCase().replace(" ", "_"),
- name);
+ "label.colourScheme_", name.toLowerCase().replace(" ", "_"));
final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
label);
radioItem.setName(name);
jGroup.setTextCol2(sg.textColour2.getRGB());
jGroup.setTextColThreshold(sg.thresholdTextColour);
jGroup.setShowUnconserved(sg.getShowNonconserved());
- jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+ jGroup.setIgnoreGapsinConsensus(sg.isIgnoreGapsConsensus());
jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
view.getIgnoreGapsinConsensus());
af.viewport.getResidueShading()
- .setConsensus(af.viewport.getSequenceConsensusHash());
+ .setConsensus(af.viewport.getConsensusProfiles());
af.viewport.setColourAppliesToAllGroups(false);
if (view.getConservationSelected() && cs != null)
af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
true);
af.viewport.getResidueShading()
- .setConsensus(af.viewport.getSequenceConsensusHash());
+ .setConsensus(af.viewport.getConsensusProfiles());
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
import jalview.ws.params.ParameterI;
import jalview.ws.params.ValueConstrainI;
import jalview.ws.params.ValueConstrainI.ValueType;
+import jalview.ws.params.simple.LogarithmicParameter;
import java.awt.BorderLayout;
import java.awt.Component;
public class ParamBox extends JPanel
implements ChangeListener, ActionListener, MouseListener
{
+
+ boolean isLogarithmic;
+
boolean adjusting = false;
boolean choice = false;
choice = true;
}
}
+ if (parm instanceof LogarithmicParameter)
+ {
+ isLogarithmic = true;
+ }
if (!compact)
{
{
if (!adjusting)
{
- valueField.setText("" + ((integ) ? ("" + slider.getValue())
- : ("" + slider.getValue() / 1000f)));
+ if (!isLogarithmic)
+ {
+ valueField.setText("" + ((integ) ? ("" + slider.getValue())
+ : ("" + slider.getValue() / 1000f)));
+ }
+ else
+ {
+ Double base = ((LogarithmicParameter) parameter).getBase();
+ Double value = Math.pow(
+ base,
+ slider.getValue() / 1000000f);
+ valueField.setText(formatDouble(value));
+ }
checkIfModified();
}
}
+ public String formatDouble(Double value)
+ {
+ String string = String.format("%3.3f", value);
+ if (value < 0.001)
+ {
+ string = String.format("%3.3e", value);
+ }
+ return string;
+ }
+
public void updateControls(ParameterI parm)
{
adjusting = true;
}
else
{
- valueField.setText(parm.getValue());
+ if (parm instanceof LogarithmicParameter)
+ {
+ Double base = ((LogarithmicParameter) parm).getBase();
+ Double value = Math.pow(base,
+ Double.parseDouble(parm.getValue()) / 1000000);
+ valueField.setText(formatDouble(value));
+ }
+ else
+ {
+ valueField.setText(parm.getValue());
+ }
}
}
lastVal = updateSliderFromValueField();
{
int iVal;
float fVal;
+ double dVal;
if (validator != null)
{
if (integ)
}
return new int[] { iVal };
}
+ else if (isLogarithmic)
+ {
+ double eValue;
+ dVal = 0d;
+ try
+ {
+ valueField.setText(valueField.getText().trim());
+ eValue = Double.valueOf(valueField.getText());
+
+ dVal = Math.log(eValue) / Math
+ .log(((LogarithmicParameter) parameter).getBase())
+ * 1000000;
+
+ if (validator.getMin() != null
+ && validator.getMin().doubleValue() > dVal)
+ {
+ dVal = validator.getMin().doubleValue();
+ // TODO: provide visual indication that hard limit was reached for
+ // this parameter
+ // update value field to reflect any bound checking we performed.
+ valueField.setText("" + formatDouble(eValue));
+ }
+ if (validator.getMax() != null
+ && validator.getMax().doubleValue() < dVal)
+ {
+ dVal = validator.getMax().doubleValue();
+ // TODO: provide visual indication that hard limit was reached for
+ // this parameter
+ // update value field to reflect any bound checking we performed.
+ valueField.setText("" + formatDouble(eValue));
+ }
+ } catch (Exception e)
+ {
+ }
+ ;
+ if (validator.getMin() != null && validator.getMax() != null)
+ {
+ slider.getModel().setRangeProperties((int) (dVal), 1,
+ (int) (validator.getMin().doubleValue()),
+ 1 + (int) (validator.getMax().doubleValue()),
+ true);
+ }
+ else
+ {
+ slider.setVisible(false);
+ }
+ return new double[] { dVal };
+ }
else
{
fVal = 0f;
URL linkImageURL = getClass().getResource("/images/link.gif");
- Map<String, OptionBox> optSet = new java.util.LinkedHashMap<String, OptionBox>();
+ Map<String, OptionBox> optSet = new java.util.LinkedHashMap<>();
- Map<String, ParamBox> paramSet = new java.util.LinkedHashMap<String, ParamBox>();
+ Map<String, ParamBox> paramSet = new java.util.LinkedHashMap<>();
public Map<String, OptionBox> getOptSet()
{
*/
public List<ArgumentI> getCurrentSettings()
{
- List<ArgumentI> argSet = new ArrayList<ArgumentI>();
+ List<ArgumentI> argSet = new ArrayList<>();
for (OptionBox opts : getOptSet().values())
{
OptionI opt = opts.getOptionIfEnabled();
JMenuItem sequenceFeature = 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);
+ }
+
+
if (alignPanel.av.getSelectionGroup() != null
&& alignPanel.av.getSelectionGroup().getSize() > 1)
{
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
+ Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
SequenceI sqass = null;
for (SequenceI sq : alignPanel.av.getSequenceSelection())
jMenu1.add(displayNonconserved);
}
+
+ protected void selectHMM_actionPerformed(ActionEvent e)
+ {
+ SequenceI hmm = ap.av.getSequenceSelection()[0];
+ ap.alignFrame.setSelectedHMMSequence(hmm);
+ }
+
/**
* Constructs the entries for the colour menu
*/
import jalview.bin.Cache;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.hmmer.HmmerCommand;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.MouseEvent;
import java.io.File;
import java.util.ArrayList;
public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String HMMER_PATH = "HMMER_PATH";
+
+ public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
+
+ public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
frame.setMinimumSize(new Dimension(width, height));
/*
+ * Set HMMER tab defaults
+ */
+ hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ if (Cache.getDefault("USE_UNIPROT", false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+ hmmerPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateHMMERPath(true);
+ }
+ });
+ hmmerPath.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ validateHMMERPath(true);
+ }
+ });
+
+ /*
* Set Visual tab defaults
*/
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
showConsensLogo
.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showInformationHistogram.setSelected(
+ Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
+ showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
showNpTooltip
.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
showDbRefTooltip
Boolean.toString(showConsensHistogram.isSelected()));
Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
Boolean.toString(showConsensLogo.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
+ Boolean.toString(showConsensHistogram.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
+ Boolean.toString(showHMMLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
maxColour.getBackground());
/*
+ * Save HMMER settings
+ */
+ Cache.applicationProperties.setProperty("TRIM_TERMINI",
+ Boolean.toString(hmmrTrimTermini.isSelected()));
+ Cache.applicationProperties.setProperty("USE_UNIPROT",
+ Boolean.toString(hmmerBackgroundUniprot.isSelected()));
+ Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
+ hmmerSequenceCount.getText());
+ Cache.applicationProperties.setProperty(HMMER_PATH,
+ hmmerPath.getText());
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames != null && frames.length > 0)
+ {
+ for (AlignFrame f : frames)
+ {
+ f.updateHMMERStatus();
+ }
+ }
+
+ hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ if (Cache.getDefault("USE_UNIPROT", false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+ /*
* Save Overview settings
*/
Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
&& (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 is to a folder that contains an executable
+ * hmmbuild or hmmbuild.exe, else false (optionally after showing a warning
+ * dialog)
+ */
+ @Override
+ protected boolean validateHMMERPath(boolean showWarning)
+ {
+ String folder = hmmerPath.getText().trim();
+
+ if (HmmerCommand.getExecutable(HmmerCommand.HMMBUILD, folder) != null)
+ {
+ return true;
+ }
+ if (showWarning && folder.length() > 0)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.hmmbuild_not_found"),
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return false;
+ }
+
+ /**
+ * Checks if a file can be executed
+ *
+ * @param path
+ * the path to the file
+ * @return
+ */
+ public boolean canExecute(String path)
+ {
+ File file = new File(path);
+ if (!file.canExecute())
+ {
+ file = new File(path + ".exe");
+ {
+ if (!file.canExecute())
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
/**
* If Chimera is selected, check it can be found on default or user-specified
// always do this - annotation has own state
// but defer colourscheme update until hidden sequences are passed in
- boolean vischange = stretchGroup.recalcConservation(true);
+ boolean vischange = stretchGroup.recalcAnnotations(true);
updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
&& afterDrag;
if (stretchGroup.cs != null)
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
-import net.miginfocom.swing.MigLayout;
-
import compbio.metadata.Argument;
import compbio.metadata.Option;
import compbio.metadata.Parameter;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
+import net.miginfocom.swing.MigLayout;
/**
* job parameter editing/browsing dialog box. User can browse existing settings
this(service, null);
}
+ public WsJobParameters(JFrame parent, ParamDatastoreI store,
+ WsParamSetI preset,
+ List<ArgumentI> args)
+ {
+ super();
+ jbInit();
+ this.paramStore = store;
+ this.service = null;
+ // argSetModified(false);
+ // populate parameter table
+ init(preset, args);
+ // display in new JFrame attached to parent.
+ validate();
+ }
+
public WsJobParameters(Jws2Instance service, WsParamSetI preset)
{
this(null, service, preset, null);
{
frame = new JDialog(Desktop.instance, true);
+ if (service != null)
+ {
+ frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
+ new String[]
+ { service.getActionText() }));
+ }
- frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
- new String[]
- { service.getActionText() }));
Rectangle deskr = Desktop.instance.getBounds();
Dimension pref = this.getPreferredSize();
frame.setBounds(
// null;
}
+ init(p, jobArgset);
+
+ }
+
+ void init(WsParamSetI p, List<ArgumentI> jobArgset)
+ {
Hashtable exnames = new Hashtable();
for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
{
}
}
settingDialog = false;
-
}
@SuppressWarnings("unchecked")
int p = 0;
if (args.length > 0)
{
- Vector<String> services = new Vector<String>();
+ Vector<String> services = new Vector<>();
services.addElement(args[p++]);
Jws2Discoverer.getDiscoverer().setServiceUrls(services);
}
if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
{
final String setname = (String) setName.getSelectedItem();
- System.out.println("Item state changed for " + setname
- + " (handling ? " + !settingDialog + ")");
+ // System.out.println("Item state changed for " + setname
+ // + " (handling ? " + !settingDialog + ")");
if (settingDialog)
{
// ignore event
--- /dev/null
+package jalview.hmmer;
+
+import jalview.analysis.AlignmentSorter;
+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.SplitFrame;
+import jalview.io.DataSourceType;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.ws.params.ArgumentI;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+
+public class HMMAlign extends HmmerCommand
+{
+ static final String HMMALIGN = "hmmalign";
+
+ static final String ARG_TRIM = "--trim";
+
+ private final AlignmentI dataset;
+
+ private AlignmentView msa;
+
+ /**
+ * Constructor for the HMMAlignThread
+ *
+ * @param af
+ * @param args
+ */
+ public HMMAlign(AlignFrame af, List<ArgumentI> args)
+ {
+ super(af, args);
+ if (alignment.getDataset() != null)
+ {
+ dataset = alignment.getDataset();
+ }
+ else
+ {
+ dataset = null;
+ }
+ }
+
+ /**
+ * 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 segment of the alignment. Call this method directly to execute
+ * synchronously, or via start() in a new Thread for asynchronously.
+ */
+ @Override
+ public void run()
+ {
+ HiddenMarkovModel hmm = af.getSelectedHMM();
+ if (hmm == null)
+ {
+ System.err.println("Can't run hmmalign as no HMM profile selected");
+ return;
+ }
+
+ long msgId = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
+ msgId);
+ prepareAlignment();
+ SequenceI[][] subAlignments = msa.getVisibleContigs('-');
+
+ List<AlignmentOrder> allOrders = new ArrayList<>();
+
+ SequenceI[][] allResults = new SequenceI[subAlignments.length][];
+ int job = 0;
+ for (SequenceI[] seqs : subAlignments)
+ {
+ Hashtable sequencesHash = stashSequences(seqs);
+ try
+ {
+ File modelFile = createTempFile("hmm", ".hmm");
+ File alignmentFile = createTempFile("output", ".sto");
+ File resultFile = createTempFile("input", ".sto");
+
+ exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null);
+ exportHmm(hmm, modelFile.getAbsoluteFile());
+
+ boolean ran = runCommand(modelFile, alignmentFile, resultFile);
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmalign_failed"));
+ return;
+ }
+
+ SequenceI[] result = importData(resultFile, allOrders);
+ recoverSequences(sequencesHash, result);
+ allResults[job] = result;
+ modelFile.delete();
+ alignmentFile.delete();
+ resultFile.delete();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ job++;
+ }
+
+ displayResults(allResults, allOrders);
+
+ af.setProgressBar("", msgId);
+ }
+
+ /**
+ * Executes the hmmalign command and returns true if successful, false if an
+ * error is detected
+ *
+ * @param modelFile
+ * the HMM to align to
+ * @param alignmentFile
+ * the sequences to align
+ * @param resultFile
+ * the file to hold the results of alignment
+ * @return
+ * @throws IOException
+ */
+ private boolean runCommand(File modelFile, File alignmentFile,
+ File resultFile)
+ throws IOException
+ {
+ String command = getCommandPath(HMMALIGN);
+ if (command == null)
+ {
+ return false;
+ }
+ List<String> args = new ArrayList<>();
+ args.add(command);
+
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (MessageManager.getString("label.trim_termini").equals(name))
+ {
+ args.add(ARG_TRIM);
+ }
+ }
+ }
+ args.add("-o");
+ args.add(resultFile.getAbsolutePath());
+ args.add(modelFile.getAbsolutePath());
+ args.add(alignmentFile.getAbsolutePath());
+
+ return runCommand(args);
+ }
+
+ /**
+ * Imports the data from the file holding the output of hmmalign
+ *
+ * @param resultFile
+ * @param allOrders
+ * a list of alignment orders to add to
+ *
+ * @return
+ * @throws IOException
+ */
+ private SequenceI[] importData(File resultFile,
+ List<AlignmentOrder> allOrders) throws IOException
+ {
+ StockholmFile file = new StockholmFile(resultFile.getAbsolutePath(),
+ DataSourceType.FILE);
+ SequenceI[] result = file.getSeqsAsArray();
+ AlignmentOrder msaorder = new AlignmentOrder(result);
+ AlignmentSorter.recoverOrder(result);
+ allOrders.add(msaorder);
+
+ return result;
+ }
+
+ /**
+ * Gathers the sequences in preparation for the alignment.
+ */
+ private void prepareAlignment()
+ {
+ msa = af.gatherSequencesForAlignment();
+ }
+
+ /**
+ * Displays the results of all 'jobs' in a new frame
+ *
+ * @param allResults
+ *
+ * @param allOrders
+ */
+ private void displayResults(SequenceI[][] allResults,
+ List<AlignmentOrder> allOrders)
+ {
+ AlignmentOrder[] arrOrders = allOrders
+ .toArray(new AlignmentOrder[allOrders.size()]);
+ Object[] newview = msa.getUpdatedView(allResults, arrOrders, '-');
+ SequenceI[] seqs = (SequenceI[]) newview[0];
+ HiddenColumns hidden = (HiddenColumns) newview[1];
+ Alignment al = new Alignment(seqs);
+ al.setProperty("Alignment Program", "hmmalign");
+ if (dataset != null)
+ {
+ al.setDataset(dataset);
+ }
+
+ 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 alignFrame = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ FeatureRendererSettings featureSettings = af.getFeatureRenderer()
+ .getSettings();
+ // initialise with same renderer settings as in parent alignframe.
+ alignFrame.getFeatureRenderer().transferSettings(featureSettings);
+
+ addSortByMenuItems(alignFrame, alorders);
+
+ // 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)
+ {
+ alignFrame.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() ? alignFrame : af2, al.isNucleotide() ? af2 : alignFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+ return;
+ }
+ }
+
+ /*
+ * Not from SplitFrame, or failed to created a complementary alignment
+ */
+ Desktop.addInternalFrame(alignFrame, alignFrame.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ /**
+ * Adds sort order options to the AlignFrame menus
+ *
+ * @param alignFrame
+ * @param alorders
+ */
+ protected void addSortByMenuItems(AlignFrame alignFrame,
+ List<AlignmentOrder> alorders)
+ {
+ // update orders
+ if (alorders.size() == 1)
+ {
+ alignFrame.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++)
+ {
+ alignFrame.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
+ alorders.get(i));
+ }
+ }
+ }
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.util.MessageManager;
+import jalview.workers.InformationThread;
+import jalview.ws.params.ArgumentI;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * A class that runs the hmmbuild command as a separate process.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class HMMBuild extends HmmerCommand
+{
+ static final String ARG_AMINO = "--amino";
+
+ static final String ARG_DNA = "--dna";
+
+ static final String ARG_RNA = "--rna";
+
+ /**
+ * Constructor
+ *
+ * @param alignFrame
+ * @param args
+ */
+ public HMMBuild(AlignFrame alignFrame, List<ArgumentI> args)
+ {
+ super(alignFrame, args);
+ }
+
+ /**
+ * Builds a HMM from an alignment (and/or groups), then imports and adds it to
+ * the alignment (and/or groups). Call this method directly to execute
+ * synchronously, or via start() in a new Thread for asynchronously.
+ */
+ @Override
+ public void run()
+ {
+ long msgID = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+ msgID);
+
+ AlignViewportI viewport = af.getViewport();
+ try
+ {
+ List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (MessageManager.getString("label.hmmbuild_for").equals(name))
+ {
+ String value = arg.getValue();
+ if (MessageManager.getString("label.alignment")
+ .equals(value))
+ {
+ runBuildFor.add(alignment);
+ }
+ else if (MessageManager.getString("label.groups_and_alignment")
+ .equals(value))
+ {
+ runBuildFor.add(alignment);
+ runBuildFor.addAll(viewport.getAlignment().getGroups());
+ }
+ else if (MessageManager.getString("label.groups").equals(value))
+ {
+ runBuildFor.addAll(viewport.getAlignment().getGroups());
+ }
+ else if (MessageManager.getString("label.selected_group")
+ .equals(value))
+ {
+ runBuildFor.add(viewport.getSelectionGroup());
+ }
+ }
+ else if (MessageManager.getString("label.use_reference")
+ .equals(name))
+ {
+ // todo disable this option if no RF annotation on alignment
+ if (!af.getViewport().hasReferenceAnnotation())
+ {
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .getString("warn.no_reference_annotation"));
+ // return;
+ }
+ }
+ }
+ }
+
+ /*
+ * run hmmbuild for alignment and/or groups as selected
+ */
+ for (AnnotatedCollectionI grp : runBuildFor)
+ {
+ runHMMBuild(grp);
+ }
+ } finally
+ {
+ viewport.updateInformation(af.alignPanel);
+ af.buildColourMenu(); // to enable HMMER colour schemes
+ af.setProgressBar("", msgID);
+ }
+ }
+
+ /**
+ * Runs hmmbuild on the given sequences (alignment or group)
+ *
+ * @param grp
+ */
+ private void runHMMBuild(AnnotatedCollectionI ac)
+ {
+ File hmmFile = null;
+ File alignmentFile = null;
+ try
+ {
+ hmmFile = createTempFile("hmm", ".hmm");
+ alignmentFile = createTempFile("output", ".sto");
+ List<SequenceI> seqs = ac.getSequences();
+ List<SequenceI> copy = new ArrayList<>();
+ copy.addAll(seqs);
+
+ if (ac instanceof Alignment)
+ {
+ AlignmentI al = (Alignment) ac;
+ // todo pad gaps in an unaligned SequenceGroup as well?
+ if (!al.isAligned())
+ {
+ al.padGaps();
+ }
+ }
+
+ /*
+ * copy over sequences, excluding hmm consensus sequences
+ * hmm sequences and their Information annotation are also deleted
+ * in preparation for re-adding them when recalculated
+ */
+ Iterator<SequenceI> it = copy.iterator();
+ while (it.hasNext())
+ {
+ SequenceI seq = it.next();
+ if (seq.isHMMConsensusSequence())
+ {
+ // todo leave it to InformationThread to delete annotations?
+ AlignmentAnnotation[] seqAnnotations = seq
+ .getAnnotation();
+ if (seqAnnotations != null)
+ {
+ for (AlignmentAnnotation ann : seqAnnotations)
+ {
+ if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ alignment.deleteAnnotation(ann);
+ }
+ }
+ }
+ alignment.deleteSequence(seq);
+ it.remove();
+ }
+ }
+
+ SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
+ Hashtable sequencesHash = stashSequences(copyArray);
+
+ exportStockholm(copyArray, alignmentFile, ac);
+
+ recoverSequences(sequencesHash, seqs.toArray(new SequenceI[] {}));
+
+ boolean ran = runCommand(alignmentFile, hmmFile, ac);
+ if (!ran)
+ {
+ return;
+ }
+ importData(hmmFile, ac);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } finally
+ {
+ if (hmmFile != null)
+ {
+ hmmFile.delete();
+ }
+ if (alignmentFile != null)
+ {
+ alignmentFile.delete();
+ }
+ }
+ }
+
+ /**
+ * Constructs and executes the hmmbuild command as a separate process
+ *
+ * @param sequencesFile
+ * the alignment from which the HMM is built
+ * @param hmmFile
+ * the output file to which the HMM is written
+ * @param group
+ * alignment or group for which the hmm is generated
+ *
+ * @return
+ * @throws IOException
+ */
+ private boolean runCommand(File sequencesFile, File hmmFile,
+ AnnotatedCollectionI group) throws IOException
+ {
+ String cmd = getCommandPath(HMMBUILD);
+ if (cmd == null)
+ {
+ return false; // executable not found
+ }
+ List<String> args = new ArrayList<>();
+ args.add(cmd);
+
+ /*
+ * HMM name (will be given to consensus sequence) is
+ * - as specified by an input parameter if set
+ * - else group name with _HMM appended (if for a group)
+ * - else align fame title with _HMM appended (if title is not too long)
+ * - else "Alignment_HMM"
+ */
+ String name = "";
+
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String argName = arg.getName();
+ switch (argName)
+ {
+ case "HMM Name":
+ name = arg.getValue().trim();
+ break;
+ case "Use Reference Annotation":
+ args.add("--hand");
+ break;
+ }
+ }
+ }
+
+ if (group instanceof SequenceGroup)
+ {
+ name = ((SequenceGroup) group).getName() + "_HMM";
+ }
+
+ if ("".equals(name))
+ {
+ if (af != null && af.getTitle().length() < 15)
+ {
+ name = af.getTitle();
+ }
+ else
+ {
+ name = "Alignment_HMM";
+ }
+ }
+
+ args.add("-n");
+ args.add(name.replace(' ', '_'));
+ if (!alignment.isNucleotide())
+ {
+ args.add(ARG_AMINO); // TODO check for rna
+ }
+ else
+ {
+ args.add(ARG_DNA);
+ }
+
+ args.add(hmmFile.getAbsolutePath());
+ args.add(sequencesFile.getAbsolutePath());
+
+ return runCommand(args);
+ }
+
+ /**
+ * Imports the .hmm file produced by hmmbuild, and inserts the HMM consensus
+ * sequence (with attached HMM profile) as the first sequence in the alignment
+ * or group for which it was generated
+ *
+ * @param hmmFile
+ * @param ac
+ * (optional) the group for which the hmm was generated
+ * @throws IOException
+ */
+ private void importData(File hmmFile, AnnotatedCollectionI ac)
+ throws IOException
+ {
+ HMMFile file = new HMMFile(
+ new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
+ SequenceI[] seqs = file.getSeqsAsArray();
+ SequenceI hmmSeq = seqs[0];
+ hmmSeq.createDatasetSequence();
+ if (ac instanceof SequenceGroup)
+ {
+ SequenceGroup grp = (SequenceGroup) ac;
+ hmmSeq.insertCharAt(0, ac.getStartRes(), '-');
+ hmmSeq.insertCharAt(ac.getEndRes() + 1,
+ alignment.getWidth() - ac.getEndRes() - 1, '-');
+ hmmSeq.updateHMMMapping();
+ SequenceI topSeq = grp.getSequencesInOrder(alignment)[0];
+ int topIndex = alignment.findIndex(topSeq);
+ alignment.insertSequenceAt(topIndex, hmmSeq);
+ ac.setSeqrep(hmmSeq);
+ grp.addSequence(hmmSeq, false);
+ grp.setHmmConsensus(hmmSeq);
+ }
+ else
+ {
+ alignment.insertSequenceAt(0, hmmSeq);
+ alignment.setHmmConsensus(hmmSeq);
+ }
+
+ AlignViewport viewport = af.getViewport();
+ if (viewport != null)
+ {
+ AlignmentPanel alignPanel = viewport.getAlignPanel();
+ viewport.alignmentChanged(alignPanel);
+ alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+
+ if (alignPanel.alignFrame.getSelectedHMM() == null)
+ {
+ alignPanel.alignFrame.setSelectedHMMSequence(hmmSeq);
+ }
+ }
+ }
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.bin.Cache;
+import jalview.gui.Preferences;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.IntegerParameter;
+import jalview.ws.params.simple.LogarithmicParameter;
+import jalview.ws.params.simple.Option;
+import jalview.ws.params.simple.StringParameter;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Scanner;
+
+public class HMMERParamStore implements ParamDatastoreI
+{
+ String name;
+
+ List<WsParamSetI> presets = new ArrayList<>();
+
+ public HMMERParamStore(String nam)
+ {
+ this.name = nam;
+ }
+
+ @Override
+ public List<WsParamSetI> getPresets()
+ {
+ return presets;
+ }
+
+ @Override
+ public WsParamSetI getPreset(String nam)
+ {
+ return null;
+ }
+
+ @Override
+ public List<ArgumentI> getServiceParameters()
+ {
+ List<ArgumentI> args = new ArrayList<>();
+ if ("hmmsearch".equals(name))
+ {
+ getHMMSearchParams(args);
+ }
+ if ("hmmalign".equals(name))
+ {
+ getHMMAlignParams(args);
+
+ }
+ if ("hmmbuild".equals(name))
+ {
+ getHMMBuildParams(args);
+
+ }
+ return args;
+ }
+
+ private void getHMMSearchParams(List<ArgumentI> args)
+ {
+ args.add(new IntegerParameter(
+ MessageManager.getString("label.number_of_results"),
+ MessageManager.getString("label.number_of_results_desc"), true,
+ 100, 0, 100000));
+ String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+ if (names != null && !names.isEmpty())
+ {
+ Collection<String> databases = new ArrayList<>();
+ databases.add(MessageManager.getString("label.this_alignment"));
+ Scanner nameScanner = new Scanner(names);
+
+ if (nameScanner.hasNext())
+ {
+ while (nameScanner.hasNext())
+ {
+ String next = nameScanner.next();
+ if (next == "null")
+ {
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+ Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+ }
+ else
+ {
+ databases.add(next);
+ }
+ }
+ }
+ nameScanner.close();
+ args.add(new Option(MessageManager.getString("label.database"),
+ MessageManager.getString("label.database_for_hmmsearch"),
+ true, MessageManager.getString("label.this_alignment"),
+ MessageManager.getString("label.this_alignment"), databases,
+ null));
+ }
+ args.add(new BooleanOption(
+ MessageManager.getString("label.auto_align_seqs"),
+ MessageManager.getString("label.auto_align_seqs_desc"), false,
+ false, true, null));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.use_accessions"),
+ MessageManager.getString("label.use_accessions_desc"), false,
+ false, true, null));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"), false,
+ false, true, null));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString("label.seq_e_value"),
+ MessageManager.getString("label.seq_e_value_desc"), false, -3d,
+ -37.92977945, 1d, 10d));
+ /*
+ args.add(new DoubleParameter(
+ MessageManager.getString("label.seq_score"),
+ MessageManager.getString("label.seq_score_desc"), false,
+ 0d, 0d, 10000d));
+ */
+ args.add(new LogarithmicParameter(
+ MessageManager.getString("label.dom_e_value_desc"),
+ MessageManager.getString("label.dom_e_value_desc"), false, -3d,
+ -37.92977945, 1d, 10d));
+ /*
+ args.add(new DoubleParameter(
+ MessageManager.getString("label.dom_score"),
+ MessageManager.getString("label.dom_score_desc"), false, 0d,
+ 0d,
+ 10000d));
+ */
+ }
+
+ private void getHMMAlignParams(List<ArgumentI> args)
+ {
+ args.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"),
+ false, false, true, null));
+ }
+
+ private void getHMMBuildParams(List<ArgumentI> args)
+ {
+ args.add(new StringParameter(MessageManager.getString("label.hmm_name"),
+ MessageManager.getString("label.hmm_name_desc"), true, ""));
+ // todo only enable Use Reference Annotation if RF is present
+ args.add(new BooleanOption(
+ MessageManager.getString("label.use_reference"),
+ MessageManager.getString("label.use_reference_desc"), true,
+ true, true, null));
+
+ Collection<String> options = new ArrayList<>();
+ options.add(MessageManager.getString("label.alignment"));
+ options.add(MessageManager.getString("label.groups_and_alignment"));
+ options.add(MessageManager.getString("label.groups"));
+ options.add(MessageManager.getString("label.selected_group"));
+
+ args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
+ MessageManager.getString("label.hmmbuild_for_desc"), true,
+ MessageManager.getString("label.alignment"),
+ MessageManager.getString("label.alignment"), options, null));
+ }
+
+ @Override
+ public boolean presetExists(String name)
+ {
+ return false;
+ }
+
+ @Override
+ public void deletePreset(String name)
+ {
+ }
+
+ @Override
+ public void storePreset(String presetName, String text,
+ List<ArgumentI> jobParams)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void updatePreset(String oldName, String presetName, String text,
+ List<ArgumentI> jobParams)
+ {
+ }
+
+ @Override
+ public WsParamSetI parseServiceParameterFile(String name,
+ String description, String[] serviceURL, String parameters)
+ throws IOException
+ {
+ return null;
+ }
+
+ @Override
+ public String generateServiceParameterFile(WsParamSetI pset)
+ throws IOException
+ {
+ return null;
+ }
+
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.List;
+
+public class HMMERPreset implements WsParamSetI
+{
+
+ @Override
+ public String getName()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getDescription()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String[] getApplicableUrls()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getSourceFile()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setSourceFile(String newfile)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean isModifiable()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public List<ArgumentI> getArguments()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setArguments(List<ArgumentI> args)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.simple.BooleanOption;
+
+import java.io.BufferedReader;
+import java.io.File;
+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 javax.swing.JOptionPane;
+
+public class HMMSearch extends HmmerCommand
+{
+ static final String HMMSEARCH = "hmmsearch";
+
+ boolean realign = false;
+
+ boolean trim = false;
+
+ int seqsToReturn = Integer.MAX_VALUE;
+
+ SequenceI[] seqs;
+
+ /**
+ * Constructor for the HMMSearchThread
+ *
+ * @param af
+ */
+ public HMMSearch(AlignFrame af, List<ArgumentI> args)
+ {
+ super(af, args);
+ }
+
+ /**
+ * Runs the HMMSearchThread: 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. Call this method directly to execute
+ * synchronously, or via start() in a new Thread for asynchronously.
+ */
+ @Override
+ public void run()
+ {
+ HiddenMarkovModel hmm = af.getSelectedHMM();
+ if (hmm == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_selected_hmm"));
+ return;
+ }
+
+ SequenceI hmmSeq = af.getSelectedHMMSequence();
+ long msgId = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+ msgId);
+
+ try
+ {
+ File hmmFile = createTempFile("hmm", ".hmm");
+ File hitsAlignmentFile = createTempFile("hitAlignment", ".sto");
+ File searchOutputFile = createTempFile("searchOutput", ".sto");
+
+ exportHmm(hmm, hmmFile.getAbsoluteFile());
+
+ boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmsearch_failed"));
+ return;
+ }
+
+ importData(hmmSeq, hitsAlignmentFile, hmmFile, searchOutputFile);
+ // TODO make realignment of search results a step at this level
+ // and make it conditional on this.realign
+ } catch (IOException | InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ finally
+ {
+ af.setProgressBar("", msgId);
+ }
+ }
+
+ /**
+ * Executes an hmmsearch with the given hmm as input. The database to be
+ * searched is a local file as specified by the 'Database' parameter, or the
+ * current alignment (written to file) if none is specified.
+ *
+ * @param searchOutputFile
+ * @param hitsAlignmentFile
+ * @param hmmFile
+ *
+ * @return
+ * @throws IOException
+ */
+ private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,
+ File hmmFile) throws IOException
+ {
+ String command = getCommandPath(HMMSEARCH);
+ if (command == null)
+ {
+ return false;
+ }
+
+ List<String> args = new ArrayList<>();
+ args.add(command);
+ args.add("-o");
+ args.add(searchOutputFile.getAbsolutePath());
+ args.add("-A");
+ args.add(hitsAlignmentFile.getAbsolutePath());
+
+ boolean dbFound = false;
+ String dbPath = "";
+ File databaseFile = null;
+
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (MessageManager.getString("label.number_of_results")
+ .equals(name))
+ {
+ seqsToReturn = Integer.parseInt(arg.getValue());
+ }
+ else if (MessageManager.getString("label.auto_align_seqs")
+ .equals(name))
+ {
+ realign = true; // TODO: not used
+ }
+ else if (MessageManager.getString("label.use_accessions")
+ .equals(name))
+ {
+ args.add("--acc");
+ }
+ else if (MessageManager.getString("label.seq_e_value").equals(name))
+ {
+ args.add("--incE");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.seq_score").equals(name))
+ {
+ args.add("-incT");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.dom_e_value_desc")
+ .equals(name))
+ {
+ args.add("--incdomE");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.dom_score").equals(name))
+ {
+ args.add("--incdomT");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.trim_termini")
+ .equals(name))
+ {
+ trim = true;
+ }
+ else if (MessageManager.getString("label.database").equals(name))
+ {
+ dbFound = true;
+ dbPath = arg.getValue();
+ if (!MessageManager.getString("label.this_alignment")
+ .equals(dbPath))
+ {
+ databaseFile = new File(dbPath);
+ }
+ }
+ }
+ }
+
+ if (!dbFound || MessageManager.getString("label.this_alignment")
+ .equals(dbPath))
+ {
+ AlignmentI alignment = af.getViewport().getAlignment();
+ AlignmentI copy = new Alignment(alignment);
+ SequenceI hmms = copy.getHmmConsensus();
+ if (hmms != null)
+ {
+ copy.deleteSequence(hmms);
+ }
+ StockholmFile stoFile = new StockholmFile(copy);
+ stoFile.setSeqs(copy.getSequencesArray());
+ String alignmentString = stoFile.print();
+ databaseFile = createTempFile("database", ".sto");
+ PrintWriter writer = new PrintWriter(databaseFile);
+ writer.print(alignmentString);
+ writer.close();
+ }
+
+ args.add(hmmFile.getAbsolutePath());
+ args.add(databaseFile.getAbsolutePath());
+
+ return runCommand(args);
+ }
+
+ /**
+ * Imports the data from the temporary file to which the output of hmmsearch
+ * is directed.
+ *
+ * @param hmmSeq
+ */
+ private void importData(SequenceI hmmSeq, File inputAlignmentTemp,
+ File hmmTemp, File searchOutputFile)
+ throws IOException, InterruptedException
+ {
+ BufferedReader br = new BufferedReader(
+ new FileReader(inputAlignmentTemp));
+ try
+ {
+ if (br.readLine() == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("label.no_sequences_found"));
+ return;
+ }
+ StockholmFile file = new StockholmFile(new FileParse(
+ inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
+ seqs = file.getSeqsAsArray();
+
+ readTable(searchOutputFile);
+
+ int seqCount = Math.min(seqs.length, seqsToReturn);
+ SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
+ hmmAndSeqs[0] = hmmSeq;
+ System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
+
+ AlignmentI alignment = new Alignment(hmmAndSeqs);
+ AlignFrame frame = new AlignFrame(alignment, 1, 1);
+ frame.setSelectedHMMSequence(hmmSeq);
+ List<ArgumentI> alignArgs = new ArrayList<>();
+ if (trim)
+ {
+ alignArgs.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"), true,
+ true, true, null));
+ }
+ HMMAlign hmmalign = new HMMAlign(frame, alignArgs);
+ hmmalign.run();
+ frame = null;
+ hmmTemp.delete();
+ inputAlignmentTemp.delete();
+ searchOutputFile.delete();
+ } finally
+ {
+ if (br != null)
+ {
+ br.close();
+ }
+ }
+ }
+
+ void readTable(File inputTableTemp) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
+ String line = "";
+ while (!line.startsWith("Query:"))
+ {
+ line = br.readLine();
+ }
+ for (int i = 0; i < 5; i++)
+ {
+ line = br.readLine();
+ }
+
+ int index = 0;
+ while (!" ------ inclusion threshold ------".equals(line)
+ && !"".equals(line))
+ {
+ Scanner scanner = new Scanner(line);
+
+ String str = scanner.next(); // full sequence eValue score
+ float eValue = Float.parseFloat(str);
+ int seqLength = seqs[index].getLength();
+ Annotation[] annots = new Annotation[seqLength];
+ for (int j = 0; j < seqLength; j++)
+ {
+ annots[j] = new Annotation(eValue);
+ }
+ AlignmentAnnotation annot = new AlignmentAnnotation("E-value",
+ "Score", annots);
+ annot.setScore(Double.parseDouble(str));
+ annot.setSequenceRef(seqs[index]);
+ seqs[index].addAlignmentAnnotation(annot);
+
+ scanner.close();
+ line = br.readLine();
+ index++;
+ }
+
+ br.close();
+ }
+
+}
--- /dev/null
+package jalview.hmmer;
+
+import jalview.analysis.SeqsetUtils;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.gui.Preferences;
+import jalview.io.HMMFile;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+
+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;
+
+/**
+ * Base class for hmmbuild, hmmalign and hmmsearch
+ *
+ * @author TZVanaalten
+ *
+ */
+public abstract class HmmerCommand implements Runnable
+{
+ public static final String HMMBUILD = "hmmbuild";
+
+ protected final AlignFrame af;
+
+ protected final AlignmentI alignment;
+
+ protected final List<ArgumentI> params;
+
+ /**
+ * Constructor
+ *
+ * @param alignFrame
+ * @param args
+ */
+ public HmmerCommand(AlignFrame alignFrame, List<ArgumentI> args)
+ {
+ af = alignFrame;
+ alignment = af.getViewport().getAlignment();
+ params = args;
+ }
+
+ public static boolean isHmmerAvailable()
+ {
+ File exec = getExecutable(HMMBUILD, Cache.getProperty(Preferences.HMMER_PATH));
+ return exec != null;
+ }
+
+ /**
+ * Uniquifies the sequences when exporting and stores their details in a
+ * hashtable
+ *
+ * @param seqs
+ */
+ protected Hashtable stashSequences(SequenceI[] seqs)
+ {
+ return SeqsetUtils.uniquify(seqs, true);
+ }
+
+ /**
+ * Restores the sequence data lost by uniquifying
+ *
+ * @param hashtable
+ * @param seqs
+ */
+ protected void recoverSequences(Hashtable hashtable, SequenceI[] seqs)
+ {
+ SeqsetUtils.deuniquify(hashtable, seqs);
+ }
+
+ /**
+ * Runs a command as a separate process and waits for it to complete. Answers
+ * true if the process return status is zero, else false.
+ *
+ * @param command
+ * the executable command and any arguments to it
+ * @throws IOException
+ */
+ public boolean runCommand(List<String> command)
+ throws IOException
+ {
+ try
+ {
+ ProcessBuilder pb = new ProcessBuilder(command);
+ pb.redirectErrorStream(true); // merge syserr to sysout
+ final Process p = pb.start();
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ BufferedReader input = new BufferedReader(
+ new InputStreamReader(p.getInputStream()));
+ try
+ {
+ String line = input.readLine();
+ while (line != null)
+ {
+ System.out.println(line);
+ line = input.readLine();
+ }
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }).start();
+
+ p.waitFor();
+ return p.exitValue() == 0; // 0 is success, by convention
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ return false;
+ }
+ }
+
+ /**
+ * Exports an alignment (and possibly annotation) to the specified file, in
+ * Stockholm format
+ *
+ * @param seqs
+ * @param toFile
+ * @param annotated
+ * @throws IOException
+ */
+ public void exportStockholm(SequenceI[] seqs, File toFile,
+ AnnotatedCollectionI annotated)
+ throws IOException
+ {
+ if (seqs != null)
+ {
+ AlignmentI newAl = new Alignment(seqs);
+ if (toFile != null && annotated != null)
+ {
+ for (AlignmentAnnotation annot : annotated.getAlignmentAnnotation())
+ {
+ if (annot.label.contains("Reference") || "RF".equals(annot.label))
+ {
+ AlignmentAnnotation newRF;
+ if (annot.annotations.length > newAl.getWidth())
+ {
+ Annotation[] rfAnnots = new Annotation[newAl.getWidth()];
+ System.arraycopy(annot.annotations, 0, rfAnnots, 0,
+ rfAnnots.length);
+ newRF = new AlignmentAnnotation("RF", "Reference Positions",
+ rfAnnots);
+ }
+ else
+ {
+ newRF = new AlignmentAnnotation(annot);
+ }
+ newAl.addAnnotation(newRF);
+ }
+ }
+ }
+
+ StockholmFile file = new StockholmFile(newAl);
+ String output = file.print(seqs, false);
+ PrintWriter writer = new PrintWriter(toFile);
+ writer.println(output);
+ writer.close();
+ }
+ }
+
+ /**
+ * Answers the full path to the given hmmer executable, or null if file cannot
+ * be found or is not executable
+ *
+ * @param cmd
+ * command short name e.g. hmmalign
+ * @return
+ */
+ protected String getCommandPath(String cmd)
+ {
+ String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH);
+ File file = getExecutable(cmd, binariesFolder);
+ if (file == null && af != null)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmm_command_failed"));
+ }
+
+ return file == null ? null : file.getAbsolutePath();
+ }
+
+ /**
+ * Answers the executable file for the given hmmer command, or null if not
+ * found or not executable. The path to the executable is the command name
+ * prefixed by the hmmer binaries folder path, optionally with .exe appended.
+ *
+ * @param cmd
+ * hmmer command short name, for example hmmbuild
+ * @param binaryPath
+ * parent folder containing hmmer executables
+ * @return
+ */
+ public static File getExecutable(String cmd, String binaryPath)
+ {
+ File file = new File(binaryPath, cmd);
+ if (!file.canExecute())
+ {
+ file = new File(binaryPath, cmd + ".exe");
+ {
+ if (!file.canExecute())
+ {
+ file = null;
+ }
+ }
+ }
+ return file;
+ }
+
+ /**
+ * A convenience method to create a temporary file that is deleted on exit of
+ * the JVM
+ *
+ * @param prefix
+ * @param suffix
+ * @return
+ * @throws IOException
+ */
+ protected File createTempFile(String prefix, String suffix)
+ throws IOException
+ {
+ File f = File.createTempFile(prefix, suffix);
+ f.deleteOnExit();
+ return f;
+
+ }
+
+ /**
+ * Exports an HMM to the specified file
+ *
+ * @param hmm
+ * @param hmmFile
+ * @throws IOException
+ */
+ public void exportHmm(HiddenMarkovModel hmm, File hmmFile)
+ throws IOException
+ {
+ if (hmm != null)
+ {
+ HMMFile file = new HMMFile(hmm);
+ PrintWriter writer = new PrintWriter(hmmFile);
+ writer.print(file.print());
+ writer.close();
+ }
+ }
+}
*/
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.api.FeaturesSourceI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
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);
+ seq.setIsHMMConsensusSequence(true);
+ AlignmentAnnotation[] annots = viewport.getAlignment()
+ .getAlignmentAnnotation();
+ for (AlignmentAnnotation annot : annots)
+ {
+ if ("RF".equals(annot.label)
+ || annot.label.contains("Reference"))
+ {
+ seq.mapToReference(annot);
+ break;
+ }
+ }
+ alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+ alignment.insertSequenceAt(0, seq);
+ viewport.getAlignPanel().adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+
+ }
}
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
+{
+ private static final String TERMINATOR = "//";
+
+ /*
+ * keys to data in HMM file, used to store as properties of the HiddenMarkovModel
+ */
+ public static final String HMM = "HMM";
+
+ public static final String NAME = "NAME";
+
+ public static final String ACCESSION_NUMBER = "ACC";
+
+ public static final String DESCRIPTION = "DESC";
+
+ public static final String LENGTH = "LENG";
+
+ public static final String MAX_LENGTH = "MAXL";
+
+ public static final String ALPHABET = "ALPH";
+
+ public static final String DATE = "DATE";
+
+ public static final String COMMAND_LOG = "COM";
+
+ public static final String NUMBER_OF_SEQUENCES = "NSEQ";
+
+ public static final String EFF_NUMBER_OF_SEQUENCES = "EFFN";
+
+ public static final String CHECK_SUM = "CKSUM";
+
+ public static final String STATISTICS = "STATS";
+
+ public static final String COMPO = "COMPO";
+
+ public static final String GATHERING_THRESHOLD = "GA";
+
+ public static final String TRUSTED_CUTOFF = "TC";
+
+ public static final String NOISE_CUTOFF = "NC";
+
+ public static final String VITERBI = "VITERBI";
+
+ public static final String MSV = "MSV";
+
+ public static final String FORWARD = "FORWARD";
+
+ public static final String MAP = "MAP";
+
+ public static final String REFERENCE_ANNOTATION = "RF";
+
+ public static final String CONSENSUS_RESIDUE = "CONS";
+
+ public static final String CONSENSUS_STRUCTURE = "CS";
+
+ public static final String MASKED_VALUE = "MM";
+
+ private static final String ALPH_AMINO = "amino";
+
+ private static final String ALPH_DNA = "DNA";
+
+ private static final String ALPH_RNA = "RNA";
+
+ private static final String ALPHABET_AMINO = "ACDEFGHIKLMNPQRSTVWY";
+
+ private static final String ALPHABET_DNA = "ACGT";
+
+ private static final String ALPHABET_RNA = "ACGU";
+
+ private static final int NUMBER_OF_TRANSITIONS = 7;
+
+ private static final String SPACE = " ";
+
+ /*
+ * optional guide line added to an output HMMER file, purely for readability
+ */
+ private static final String TRANSITIONTYPELINE = " m->m m->i m->d i->m i->i d->m d->d";
+
+ private static String NL = System.lineSeparator();
+
+ private HiddenMarkovModel hmm;
+
+ // number of symbols in the alphabet used in the hidden Markov model
+ private int numberOfSymbols;
+
+ /**
+ * Constructor that parses immediately
+ *
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public HMMFile(String inFile, DataSourceType type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * Constructor that parses immediately
+ *
+ * @param source
+ * @throws IOException
+ */
+ public HMMFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * Default constructor
+ */
+ public HMMFile()
+ {
+ }
+
+ /**
+ * Constructor for HMMFile used for exporting
+ *
+ * @param hmm
+ * @param exportImmediately
+ */
+ public HMMFile(HiddenMarkovModel markov)
+ {
+ hmm = markov;
+ }
+
+ /**
+ * Returns the HMM produced by parsing a HMMER3 file
+ *
+ * @return
+ */
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ /**
+ * Gets the name of the hidden Markov model
+ *
+ * @return
+ */
+ public String getName()
+ {
+ return hmm.getName();
+ }
+
+ /**
+ * Reads the data from HMM file into the HMM model
+ */
+ @Override
+ public void parse()
+ {
+ try
+ {
+ hmm = new HiddenMarkovModel();
+ parseHeaderLines(dataIn);
+ parseModel(dataIn);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Reads the header properties from a HMMER3 file and saves them in the
+ * HiddeMarkovModel. This method exits after reading the next line after the
+ * HMM line.
+ *
+ * @param input
+ * @throws IOException
+ */
+ void parseHeaderLines(BufferedReader input) throws IOException
+ {
+ boolean readingHeaders = true;
+ hmm.setFileHeader(input.readLine());
+ String line = input.readLine();
+ while (readingHeaders && line != null)
+ {
+ Scanner parser = new Scanner(line);
+ String next = parser.next();
+ if (ALPHABET.equals(next))
+ {
+ String alphabetType = parser.next();
+ hmm.setProperty(ALPHABET, alphabetType);
+ String alphabet = ALPH_DNA.equalsIgnoreCase(alphabetType)
+ ? ALPHABET_DNA
+ : (ALPH_RNA.equalsIgnoreCase(alphabetType) ? ALPHABET_RNA
+ : ALPHABET_AMINO);
+ numberOfSymbols = hmm.setAlphabet(alphabet);
+ }
+ else if (HMM.equals(next))
+ {
+ readingHeaders = false;
+ String symbols = line.substring(line.indexOf(HMM) + HMM.length());
+ numberOfSymbols = hmm.setAlphabet(symbols);
+ }
+ else if (STATISTICS.equals(next))
+ {
+ parser.next();
+ String key;
+ String value;
+ key = parser.next();
+ value = parser.next() + SPACE + SPACE + parser.next();
+ hmm.setProperty(key, value);
+ }
+ else
+ {
+ String key = next;
+ String value = parser.next();
+ while (parser.hasNext())
+ {
+ value = value + SPACE + parser.next();
+ }
+ hmm.setProperty(key, value);
+ }
+ parser.close();
+ line = input.readLine();
+ }
+ }
+
+ /**
+ * Parses the model data from the HMMER3 file. The input buffer should be
+ * positioned at the (optional) COMPO line if there is one, else at the insert
+ * emissions line for the BEGIN node of the model.
+ *
+ * @param input
+ * @throws IOException
+ */
+ void parseModel(BufferedReader input) throws IOException
+ {
+ /*
+ * specification says there must always be an HMM header (already read)
+ * and one more header (guide headings) which is skipped here
+ */
+ int nodeNo = 0;
+ String line = input.readLine();
+ while (line != null && !TERMINATOR.equals(line))
+ {
+ HMMNode node = new HMMNode();
+ hmm.addNode(node);
+ Scanner scanner = new Scanner(line);
+ String next = scanner.next();
+
+ /*
+ * expect COMPO (optional) for average match emissions
+ * or a node number followed by node's match emissions
+ */
+ if (COMPO.equals(next) || nodeNo > 0)
+ {
+ /*
+ * parse match emissions
+ */
+ double[] matches = parseDoubles(scanner, numberOfSymbols);
+ node.setMatchEmissions(matches);
+ if (!COMPO.equals(next))
+ {
+ int column = parseAnnotations(scanner, node);
+ if (column == 0)
+ {
+ /*
+ * no MAP annotation provided, just number off from 0 (begin node)
+ */
+ column = nodeNo;
+ }
+ hmm.setAlignmentColumn(node, column - 1); // node 1 <==> column 0
+ }
+ line = input.readLine();
+ }
+ scanner.close();
+
+ /*
+ * parse insert emissions
+ */
+ scanner = new Scanner(line);
+ double[] inserts = parseDoubles(scanner, numberOfSymbols);
+ node.setInsertEmissions(inserts);
+ scanner.close();
+
+ /*
+ * parse state transitions
+ */
+ line = input.readLine();
+ scanner = new Scanner(line);
+ double[] transitions = parseDoubles(scanner,
+ NUMBER_OF_TRANSITIONS);
+ node.setStateTransitions(transitions);
+ scanner.close();
+ line = input.readLine();
+
+ nodeNo++;
+ }
+ }
+
+ /**
+ * Parses the annotations on the match emission line and add them to the node.
+ * (See p109 of the HMMER User Guide (V3.1b2) for the specification.) Returns
+ * the alignment column number (base 1) that the node maps to, if provided,
+ * else zero.
+ *
+ * @param scanner
+ * @param node
+ */
+ int parseAnnotations(Scanner scanner, HMMNode node)
+ {
+ /*
+ * map from hmm node to alignment column index, if provided
+ * HMM counts columns from 1, convert to base 0 for Jalview
+ */
+ int column = 0;
+ String value;
+ if (scanner.hasNext())
+ {
+ value = scanner.next();
+ if (!"-".equals(value))
+ {
+ try
+ {
+ column = Integer.parseInt(value);
+ node.setAlignmentColumn(column - 1);
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
+ }
+ }
+
+ /*
+ * hmm consensus residue if provided, else '-'
+ */
+ if (scanner.hasNext())
+ {
+ node.setConsensusResidue(scanner.next().charAt(0));
+ }
+
+ /*
+ * RF reference annotation, if provided, else '-'
+ */
+ if (scanner.hasNext())
+ {
+ node.setReferenceAnnotation(scanner.next().charAt(0));
+ }
+
+ /*
+ * 'm' for masked position, if provided, else '-'
+ */
+ if (scanner.hasNext())
+ {
+ node.setMaskValue(scanner.next().charAt(0));
+ }
+
+ /*
+ * structure consensus symbol, if provided, else '-'
+ */
+ if (scanner.hasNext())
+ {
+ node.setConsensusStructure(scanner.next().charAt(0));
+ }
+
+ return column;
+ }
+
+ /**
+ * Fills an array of doubles parsed from an input line
+ *
+ * @param input
+ * @param numberOfElements
+ * @return
+ * @throws IOException
+ */
+ static double[] parseDoubles(Scanner input,
+ int numberOfElements) throws IOException
+ {
+ double[] values = new double[numberOfElements];
+ for (int i = 0; i < numberOfElements; i++)
+ {
+ if (!input.hasNext())
+ {
+ throw new IOException("Incomplete data");
+ }
+ String next = input.next();
+ if (next.contains("*"))
+ {
+ values[i] = Double.NEGATIVE_INFINITY;
+ }
+ else
+ {
+ double prob = Double.valueOf(next);
+ prob = Math.pow(Math.E, -prob);
+ values[i] = prob;
+ }
+ }
+ return values;
+ }
+
+ /**
+ * 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 of data to be added to the String.
+ * @return
+ */
+ String addData(int initialColumnSeparation,
+ int columnSeparation, List<String> data)
+ {
+ String line = "";
+ boolean first = true;
+ for (String value : data)
+ {
+ int sep = first ? initialColumnSeparation : columnSeparation;
+ line += String.format("%" + sep + "s", value);
+ first = false;
+ }
+ 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 an array of doubles into a list of Strings, rounded to the nearest
+ * 5th decimal place
+ *
+ * @param doubles
+ * @param noOfDecimals
+ * @return
+ */
+ List<String> doublesToStringList(double[] doubles)
+ {
+ List<String> strList = new ArrayList<>();
+ for (double value : doubles)
+ {
+ 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;
+ }
+
+ /**
+ * Appends model data in string format to the string builder
+ *
+ * @param output
+ */
+ void appendModelAsString(StringBuilder output)
+ {
+ output.append(HMM).append(" ");
+ String charSymbols = hmm.getSymbols();
+ for (char c : charSymbols.toCharArray())
+ {
+ output.append(String.format("%9s", c));
+ }
+ output.append(NL).append(TRANSITIONTYPELINE);
+
+ int length = hmm.getLength();
+
+ for (int nodeNo = 0; nodeNo <= length; nodeNo++)
+ {
+ String matchLine = String.format("%7s",
+ nodeNo == 0 ? COMPO : Integer.toString(nodeNo));
+
+ double[] doubleMatches = convertToLogSpace(
+ hmm.getNode(nodeNo).getMatchEmissions());
+ List<String> strMatches = doublesToStringList(doubleMatches);
+ matchLine += addData(10, 9, strMatches);
+
+ if (nodeNo != 0)
+ {
+ matchLine += SPACE + (hmm.getNodeAlignmentColumn(nodeNo) + 1);
+ matchLine += SPACE + hmm.getConsensusResidue(nodeNo);
+ matchLine += SPACE + hmm.getReferenceAnnotation(nodeNo);
+ if (hmm.getFileHeader().contains("HMMER3/f"))
+ {
+ matchLine += SPACE + hmm.getMaskedValue(nodeNo);
+ matchLine += SPACE + hmm.getConsensusStructure(nodeNo);
+ }
+ }
+
+ output.append(NL).append(matchLine);
+
+ String insertLine = "";
+
+ double[] doubleInserts = convertToLogSpace(
+ hmm.getNode(nodeNo).getInsertEmissions());
+ List<String> strInserts = doublesToStringList(doubleInserts);
+ insertLine += addData(17, 9, strInserts);
+
+ output.append(NL).append(insertLine);
+
+ String transitionLine = "";
+ double[] doubleTransitions = convertToLogSpace(
+ hmm.getNode(nodeNo).getStateTransitions());
+ List<String> strTransitions = doublesToStringList(
+ doubleTransitions);
+ transitionLine += addData(17, 9, strTransitions);
+
+ output.append(NL).append(transitionLine);
+ }
+ }
+
+ /**
+ * Appends formatted HMM file properties to the string builder
+ *
+ * @param output
+ */
+ void appendProperties(StringBuilder output)
+ {
+ output.append(hmm.getFileHeader());
+
+ String format = "%n%-5s %1s";
+ appendProperty(output, format, NAME);
+ appendProperty(output, format, ACCESSION_NUMBER);
+ appendProperty(output, format, DESCRIPTION);
+ appendProperty(output, format, LENGTH);
+ appendProperty(output, format, MAX_LENGTH);
+ appendProperty(output, format, ALPHABET);
+ appendBooleanProperty(output, format, REFERENCE_ANNOTATION);
+ appendBooleanProperty(output, format, MASKED_VALUE);
+ appendBooleanProperty(output, format, CONSENSUS_RESIDUE);
+ appendBooleanProperty(output, format, CONSENSUS_STRUCTURE);
+ appendBooleanProperty(output, format, MAP);
+ appendProperty(output, format, DATE);
+ appendProperty(output, format, NUMBER_OF_SEQUENCES);
+ appendProperty(output, format, EFF_NUMBER_OF_SEQUENCES);
+ appendProperty(output, format, CHECK_SUM);
+ appendProperty(output, format, GATHERING_THRESHOLD);
+ appendProperty(output, format, TRUSTED_CUTOFF);
+ appendProperty(output, format, NOISE_CUTOFF);
+
+ if (hmm.getMSV() != null)
+ {
+ format = "%n%-19s %18s";
+ output.append(String.format(format, "STATS LOCAL MSV", hmm.getMSV()));
+
+ output.append(String.format(format, "STATS LOCAL VITERBI",
+ hmm.getViterbi()));
+
+ output.append(String.format(format, "STATS LOCAL FORWARD",
+ hmm.getForward()));
+ }
+ }
+
+ /**
+ * Appends 'yes' or 'no' for the given property, according to whether or not
+ * it is set in the HMM
+ *
+ * @param output
+ * @param format
+ * @param propertyName
+ */
+ private void appendBooleanProperty(StringBuilder output, String format,
+ String propertyName)
+ {
+ boolean set = hmm.getBooleanProperty(propertyName);
+ output.append(String.format(format, propertyName,
+ set ? HiddenMarkovModel.YES : HiddenMarkovModel.NO));
+ }
+
+ /**
+ * Appends the value of the given property to the output, if not null
+ *
+ * @param output
+ * @param format
+ * @param propertyName
+ */
+ private void appendProperty(StringBuilder output, String format,
+ String propertyName)
+ {
+ String value = hmm.getProperty(propertyName);
+ if (value != null)
+ {
+ output.append(String.format(format, propertyName, value));
+ }
+ }
+
+ @Override
+ public String print(SequenceI[] sequences, boolean jvsuffix)
+ {
+ if (sequences[0].getHMM() != null)
+ {
+ hmm = sequences[0].getHMM();
+ }
+ return print();
+ }
+
+ /**
+ * Prints the .hmm file to a String.
+ *
+ * @return
+ */
+ public String print()
+ {
+ StringBuilder output = new StringBuilder();
+ appendProperties(output);
+ output.append(NL);
+ appendModelAsString(output);
+ output.append(NL).append(TERMINATOR).append(NL);
+ return output.toString();
+ }
+
+ /**
+ * Converts the probabilities contained in an array into log space
+ *
+ * @param ds
+ */
+ double[] convertToLogSpace(double[] ds)
+ {
+ double[] converted = new double[ds.length];
+ for (int i = 0; i < ds.length; i++)
+ {
+ double prob = ds[i];
+ double logProb = -1 * Math.log(prob);
+
+ converted[i] = logProb;
+ }
+ return converted;
+ }
+
+ /**
+ * 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;
+ }
+
+ @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);
}
{
label = aa.label;
}
+ else if ("RF".equals(key))
+ {
+ label = key;
+ }
else
{
label = key + "_cons";
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 jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
+import jalview.hmmer.HmmerCommand;
+import jalview.io.FileFormatException;
import jalview.io.FileFormats;
import jalview.util.MessageManager;
import jalview.util.Platform;
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 JMenu hmmAlign = new JMenu();
+
+ protected JMenuItem hmmAlignRun = new JMenuItem();
+
+ protected JMenuItem hmmAlignSettings = new JMenuItem();
+
+ protected JMenu hmmSearch = new JMenu();
+
+ protected JMenuItem hmmSearchRun = new JMenuItem();
+
+ protected JMenuItem hmmSearchSettings = new JMenuItem();
+
+ protected JMenuItem addDatabase = new JMenuItem();
+
+ protected JMenu hmmBuild = new JMenu();
+
+ protected JMenuItem hmmBuildRun = new JMenuItem();
+
+ protected JMenuItem hmmBuildSettings = new JMenuItem();
+
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"));
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+ hmmerMenu.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmerMenu_actionPerformed(e);
+ }
+ });
+ hmmerMenu.add(hmmBuild);
+ hmmerMenu.add(hmmAlign);
+ hmmerMenu.add(hmmSearch);
+
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();
+ }
}
});
loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
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);
}
};
+ hmmBuildRun.setText(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmbuild"));
+ hmmBuildRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuildRun_actionPerformed();
+ }
+ });
+ hmmBuildSettings.setText(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmBuildSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmBuildSettings_actionPerformed();
+ }
+ });
+ hmmAlignRun.setText(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmalign"));
+ hmmAlignRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlignRun_actionPerformed();
+ }
+ });
+ hmmAlignSettings.setText(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmAlignSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmAlignSettings_actionPerformed();
+ }
+ });
+ hmmSearchRun.setText(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmsearch"));
+ hmmSearchRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearchRun_actionPerformed();
+ }
+ });
+ addDatabase.setText(MessageManager.getString("label.add_database"));
+ addDatabase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ addDatabase_actionPerformed();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ hmmSearchSettings.setText(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmSearchSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hmmSearchSettings_actionPerformed();
+ }
+ });
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(loadVcf);
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 JMenu(MessageManager.getString("label.hmmalign"));
+ hmmAlignSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmalign"));
+ hmmAlign.add(hmmAlignSettings);
+ hmmAlign.add(hmmAlignRun);
+ hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+ hmmBuildSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmbuild"));
+ hmmBuild.add(hmmBuildSettings);
+ hmmBuild.add(hmmBuildRun);
+ hmmSearch = new JMenu(MessageManager.getString("label.hmmsearch"));
+ hmmSearchSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "hmmsearch"));
+ addDatabase = new JMenuItem(
+ MessageManager.getString("label.add_database"));
+ hmmSearch.add(hmmSearchSettings);
+ hmmSearch.add(hmmSearchRun);
+ hmmSearch.add(addDatabase);
+ }
+
protected void loadVcf_actionPerformed()
{
}
}
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
{
}
+ protected void hmmBuildRun_actionPerformed()
+ {
+ }
+
+ protected void hmmSearchRun_actionPerformed()
+ {
+ }
+
+ protected void addDatabase_actionPerformed()
+ throws FileFormatException, IOException
+ {
+ }
+
+ protected void hmmAlignRun_actionPerformed()
+ {
+ }
+
+ protected void hmmBuildSettings_actionPerformed()
+ {
+ }
+
+ protected void hmmSearchSettings_actionPerformed()
+ {
+ }
+
+ protected void hmmAlignSettings_actionPerformed()
+ {
+ }
+
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.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
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 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 sortByTree = new JCheckBox();
/*
+ * hmmer tab and components
+ */
+ protected JPanel hmmerTab = new JPanel();
+
+ protected JCheckBox hmmrTrimTermini = new JCheckBox();
+
+ protected AbstractButton hmmerBackgroundUniprot = new JCheckBox();
+
+ protected AbstractButton hmmerBackgroundAlignment = new JCheckBox();
+
+ protected JTextField hmmerSequenceCount = new JTextField();
+
+ protected JTextField hmmerPath = new JTextField();
+
+ /*
* 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.
*/
/*
* Handler to validate a tab before leaving it - currently only for
- * Structure.
+ * Structure
*/
tabbedPane.addChangeListener(new ChangeListener()
{
}
/**
+ * Initialises the hmmer tabbed panel
+ *
+ * @return
+ */
+ private JPanel initHMMERTab()
+ {
+ hmmerTab.setLayout(null);
+
+ JLabel installationLocation = new JLabel(
+ MessageManager.getString("label.hmmer_location"));
+ installationLocation.setFont(LABEL_FONT);
+ installationLocation.setBounds(new Rectangle(22, 10, 250, 23));
+ hmmerPath.setBounds(new Rectangle(22, 30, 300, 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);
+ }
+ }
+ }
+ });
+
+ JLabel hmmalign = new JLabel(
+ MessageManager.getString("label.hmmalign_label"));
+ hmmalign.setFont(LABEL_FONT);
+ hmmalign.setBounds(new Rectangle(22, 50, 200, 23));
+
+ hmmrTrimTermini.setFont(LABEL_FONT);
+ hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+ hmmrTrimTermini.setBounds(new Rectangle(22, 70, 200, 23));
+
+ JLabel hmmsearch = new JLabel(
+ MessageManager.getString("label.hmmsearch_label"));
+ hmmsearch.setFont(LABEL_FONT);
+ hmmsearch.setBounds(new Rectangle(22, 90, 200, 23));
+
+ JLabel sequencesToKeep = new JLabel(
+ MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setFont(LABEL_FONT);
+ sequencesToKeep.setBounds(new Rectangle(22, 110, 125, 23));
+ hmmerSequenceCount.setBounds(new Rectangle(150, 110, 40, 23));
+
+ ButtonGroup backgroundFreqSource = new ButtonGroup();
+ backgroundFreqSource.add(hmmerBackgroundUniprot);
+ backgroundFreqSource.add(hmmerBackgroundAlignment);
+ backgroundFreqSource.setSelected(hmmerBackgroundUniprot.getModel(), true);
+
+ hmmerBackgroundUniprot.setText(MessageManager.getString("label.freq_uniprot"));
+ hmmerBackgroundUniprot.setFont(LABEL_FONT);
+ hmmerBackgroundUniprot.setBounds(new Rectangle(22, 130, 255, 23));
+
+ hmmerBackgroundAlignment.setText(MessageManager.getString("label.freq_alignment"));
+ hmmerBackgroundAlignment.setFont(LABEL_FONT);
+ hmmerBackgroundAlignment.setBounds(new Rectangle(22, 150, 300, 23));
+
+ hmmerTab.add(hmmerBackgroundUniprot);
+ hmmerTab.add(hmmerBackgroundAlignment);
+ hmmerTab.add(hmmalign);
+ hmmerTab.add(hmmsearch);
+ hmmerTab.add(installationLocation);
+ hmmerTab.add(hmmerPath);
+ hmmerTab.add(hmmrTrimTermini);
+ hmmerTab.add(sequencesToKeep);
+ hmmerTab.add(sequencesToKeep);
+ hmmerTab.add(hmmerSequenceCount);
+
+ 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 choice;
}
- /**
- * Validate the structure tab preferences; if invalid, set focus on this tab.
- *
- * @param e
- */
- protected boolean validateStructure(FocusEvent e)
+ protected boolean validateStructure()
{
- if (!validateStructure())
- {
- e.getComponent().requestFocusInWindow();
- return false;
- }
- return true;
+ return false;
}
- protected boolean validateStructure()
+ protected boolean validateHMMERPath(boolean showWarning)
{
return false;
}
}
}
+
+ 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;
import jalview.schemes.ResidueProperties;
import jalview.schemes.ZappoColourScheme;
import jalview.util.Platform;
+import jalview.workers.InformationThread;
import java.awt.BasicStroke;
import java.awt.Color;
private final boolean MAC = Platform.isAMac();
- boolean av_renderHistogram = true, av_renderProfile = true,
- av_normaliseProfile = false;
+ // todo remove these flags, read from group/viewport where needed
+ boolean av_renderHistogram = true;
+
+ boolean av_renderProfile = true;
+
+ boolean av_normaliseProfile = false;
+
+ boolean av_infoHeight = false;
ResidueShaderI profcolour = null;
private boolean av_ignoreGapsConsensus;
+ private boolean av_ignoreBelowBackground;
+
/**
* attributes set from AwtRenderPanelI
*/
}
columnSelection = av.getColumnSelection();
hiddenColumns = av.getAlignment().getHiddenColumns();
- hconsensus = av.getSequenceConsensusHash();
+ hconsensus = av.getConsensusProfiles();
complementConsensus = av.getComplementConsensusHash();
hStrucConsensus = av.getRnaStructureConsensusHash();
av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
+ av_ignoreBelowBackground = av.isIgnoreBelowBackground();
+ av_infoHeight = av.isInfoLetterHeight();
}
+
+
/**
* 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 (InformationThread.HMM_CALC_ID.equals(aa.getCalcId()))
+ {
+ HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
+ return AAFrequency.extractHMMProfile(hmm, column,
+ av_ignoreBelowBackground, av_infoHeight); // 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
+ if (aa.groupRef != null && aa.groupRef.getConsensusData() != null
&& aa.groupRef.isShowSequenceLogo())
{
// TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
- aa.groupRef.consensusData.get(column),
- aa.groupRef.getIgnoreGapsConsensus());
+ aa.groupRef.getConsensusData().get(column),
+ aa.groupRef.isIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
// be stored
renderProfile = av_renderProfile;
normaliseProfile = av_normaliseProfile;
}
+ else if (InformationThread.HMM_CALC_ID.equals(row.getCalcId()))
+ {
+ if (row.groupRef != null)
+ {
+ renderHistogram = row.groupRef.isShowInformationHistogram();
+ renderProfile = row.groupRef.isShowHMMSequenceLogo();
+ normaliseProfile = row.groupRef.isNormaliseHMMSequenceLogo();
+ }
+ else
+ {
+ renderHistogram = av.isShowInformationHistogram();
+ renderProfile = av.isShowHMMSequenceLogo();
+ normaliseProfile = av.isNormaliseHMMSequenceLogo();
+ }
+ }
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.ResidueCount;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * A colour scheme based on a selected Hidden Markov Model. The colour is
+ * <ul>
+ * <li>white for a gap</li>
+ * <li>red for an insertion</li>
+ * <li>orange for negative information content</li>
+ * <li>white to blue for increasing information content</li>
+ * </ul>
+ * where information content is the log ratio
+ *
+ * <pre>
+ * log(profile match emission probability / residue background probability>
+ * </pre>
+ *
+ * using the alignment's background frequencies for residues.
+ *
+ * @author tzvanaalten
+ *
+ */
+public class HMMERAlignmentColourScheme extends ResidueColourScheme
+{
+ /*
+ * the ratio, for each symbol, of its frequency to total symbol count
+ */
+ Map<Character, Double> frequency = new HashMap<>();
+
+ float logTotalCount;
+
+ HiddenMarkovModel hmm;
+
+ /**
+ * Constructor given a Hidden Markov Model
+ *
+ * @param sg
+ *
+ * @param markov
+ */
+ public HMMERAlignmentColourScheme(AnnotatedCollectionI sg,
+ HiddenMarkovModel markov)
+ {
+ hmm = markov;
+ countFrequencies(sg);
+ }
+
+ /**
+ * Default constructor (required by ColourSchemes.loadColourSchemes)
+ */
+ public HMMERAlignmentColourScheme()
+ {
+ }
+
+ @Override
+ public Color findColour(char symbol, int position, SequenceI seq,
+ String consensusResidue, float pid)
+ {
+ return findColour(symbol, position);
+ }
+
+ /**
+ * Returns the colour at a particular symbol at a column in the alignment:
+ * <ul>
+ * <li>white for a gap</li>
+ * <li>red for an insertion</li>
+ * <li>orange for negative information content</li>
+ * <li>white to blue for increasing information content</li>
+ * </ul>
+ *
+ * @param symbol
+ * @param column
+ * @return
+ */
+ private Color findColour(char symbol, int column)
+ {
+ if (hmm == null || Comparison.isGap(symbol))
+ {
+ return Color.white;
+ }
+ if (Character.isLowerCase(symbol))
+ {
+ symbol = Character.toUpperCase(symbol);
+ }
+ double prob = hmm.getMatchEmissionProbability(column, symbol);
+ Double freq = frequency.get(symbol);
+ if (freq == null)
+ {
+ return Color.white;
+ }
+ if (prob == 0)
+ {
+ return new Color(230, 0, 0);
+ }
+ double value = Math.log(prob / freq.doubleValue());
+ Color colour = null;
+ if (value > 0)
+ {
+ colour = ColorUtils.getGraduatedColour((float) value, 0,
+ Color.WHITE, logTotalCount, Color.blue);
+ }
+ else if (value < 0)
+ {
+ return Color.ORANGE;
+ }
+ return colour;
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI collection,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ /*
+ * ? no need to do anything if alignment is adjusted
+ * since findColour() handles everything
+ */
+ }
+
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ SequenceI hmmSeq = sg.getHmmConsensus();
+ HiddenMarkovModel model = hmmSeq == null ? null : hmmSeq.getHMM();
+ return new HMMERAlignmentColourScheme(sg, model);
+ }
+
+ /**
+ * Answers true if the sequence collection has an HMM consensus sequence, else
+ * false
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ return ac.getHmmConsensus() != null;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.HMMERA.toString();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+
+ /**
+ * Counts and stores the relatively frequency of every residue in the
+ * alignment
+ *
+ * @param sg
+ */
+ public void countFrequencies(AnnotatedCollectionI sg)
+ {
+ ResidueCount counts = new ResidueCount(sg.getSequences());
+ int total = counts.getTotalResidueCount(); // excludes gaps
+
+ for (char symbol : counts.getSymbolCounts().symbols)
+ {
+ double freq = counts.getCount(symbol) / (double) total;
+ frequency.put(symbol, freq);
+ }
+ logTotalCount = (float) Math.log(total);
+ }
+}
--- /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.Map;
+
+/**
+ * A colour scheme based on a selected Hidden Markov Model. The colour is
+ * <ul>
+ * <li>white for a gap</li>
+ * <li>red for an insertion</li>
+ * <li>orange for negative information content</li>
+ * <li>white to blue for increasing information content</li>
+ * </ul>
+ * where information content is the log ratio
+ *
+ * <pre>
+ * log(profile match emission probability / residue background probability>
+ * </pre>
+ *
+ * using global ('Uniprot') background frequencies for residues.
+ *
+ * @author tzvanaalten
+ *
+ */
+public class HMMERColourScheme extends ResidueColourScheme
+{
+ /*
+ * The highest possible log ratio is when match emission probability in
+ * the HMM model is 1, and background (for W) is 0.0109 giving
+ * log(1/0.0109) = log(91.743) = 4.519
+ */
+ private static final float MAX_LOG_RATIO = 4.519f;
+
+ private static final Color REDDISH = new Color(230, 0, 0);
+
+ HiddenMarkovModel hmm;
+
+ /**
+ * Constructor given a Hidden Markov Model
+ *
+ * @param markov
+ */
+ public HMMERColourScheme(HiddenMarkovModel markov)
+ {
+ hmm = markov;
+ }
+
+ /**
+ * Default constructor (required by ColourSchemes.loadColourSchemes)
+ */
+ public HMMERColourScheme()
+ {
+ }
+
+ @Override
+ public Color findColour(char symbol, int position, SequenceI seq,
+ String consensusResidue, float pid)
+ {
+ return findColour(symbol, position);
+ }
+
+ /**
+ * Returns the colour at a particular symbol at a column in the alignment:
+ * <ul>
+ * <li>white for a gap</li>
+ * <li>red for an insertion</li>
+ * <li>orange for negative information content</li>
+ * <li>white to blue for increasing information content</li>
+ * </ul>
+ *
+ * @param symbol
+ * @param column
+ * @return
+ */
+ private Color findColour(char symbol, int column)
+ {
+ if (hmm == null || Comparison.isGap(symbol))
+ {
+ return Color.white;
+ }
+ if (Character.isLowerCase(symbol))
+ {
+ symbol = Character.toUpperCase(symbol);
+ }
+
+ double prob = hmm.getMatchEmissionProbability(column, symbol);
+ Float freq = 0f;
+ String alpha = hmm.getAlphabetType();
+ if (!ResidueProperties.backgroundFrequencies.get(alpha)
+ .containsKey(symbol))
+ {
+ return Color.WHITE;
+ }
+ else
+ {
+ freq = ResidueProperties.backgroundFrequencies.get(alpha).get(symbol);
+ }
+ if (prob == 0D)
+ {
+ return REDDISH;
+ }
+ double value = Math.log(prob / freq.floatValue());
+ Color colour = null;
+ if (value > 0)
+ {
+ colour = ColorUtils.getGraduatedColour((float) value, 0,
+ Color.WHITE, MAX_LOG_RATIO, Color.blue);
+ }
+ else if (value < 0)
+ {
+ return Color.ORANGE;
+ }
+ return colour;
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI collection,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ /*
+ * ? no need to do anything if alignment is adjusted
+ * since findColour() handles everything
+ */
+ }
+
+ /**
+ * Answers a new colour scheme instance based on the HMM of the first sequence
+ * in sg that has an HMM
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ SequenceI hmmSeq = sg.getHmmConsensus();
+ HiddenMarkovModel model = hmmSeq == null ? null : hmmSeq.getHMM();
+
+ HMMERColourScheme colour = new HMMERColourScheme(model);
+ return colour;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.HMMERU.toString();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+
+ /**
+ * Answers true if the sequence collection has an HMM consensus sequence, else
+ * false
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ return ac.getHmmConsensus() != null;
+ }
+
+}
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),
+ HMMERU("HMMER-Uniprot", HMMERColourScheme.class),
+ HMMERA("HMMER-Alignment", HMMERAlignmentColourScheme.class);
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
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
{
aaIndex = new int[255];
}
+ 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: these don't match https://www.ebi.ac.uk/uniprot/TrEMBLstats - what
+ // are they?
+ }
+
+ // 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);
--- /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(int minCount, int maxCount, 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();
+ if (count >= minCount && count < maxCount)
+ {
+ 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();
+ int minCount = inputScanner.nextInt();
+ int maxCount = inputScanner.nextInt();
+ boolean keepRaw = inputScanner.nextBoolean();
+ boolean forClans = inputScanner.nextBoolean();
+ analyser.runToEnd(minCount, maxCount, 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.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<>();
+ protected String sequenceSetID;
+
+ /*
+ * probably unused indicator that view is of a dataset rather than an
+ * alignment
+ */
+ protected boolean isDataset = false;
+
+ private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+
+ protected ColumnSelection colSel = new ColumnSelection();
+
+ public boolean autoCalculateConsensus = true;
+
+ protected boolean autoCalculateStrucConsensus = true;
+
+ protected boolean ignoreGapsInConsensusCalculation = false;
+
+ protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
+ protected boolean infoLetterHeight = false;
+
+ protected ResidueShaderI residueShading = new ResidueShader();
+
+ protected AlignmentAnnotation consensus;
+
+ protected AlignmentAnnotation complementConsensus;
+
+ protected AlignmentAnnotation occupancy;
+
+ protected AlignmentAnnotation strucConsensus;
+
+ protected AlignmentAnnotation conservation;
+
+ protected AlignmentAnnotation quality;
+
/**
- * alignment displayed in the viewport. Please use get/setter
+ * alignment displayed in the viewport
+ */
+ private AlignmentI alignment;
+
+ /**
+ * results of alignment consensus analysis for visible portion of view
+ */
+ protected ProfilesI consensusProfiles;
+
+ /**
+ * HMM profile for the alignment
+ */
+ protected ProfilesI hmmProfiles;
+
+ /**
+ * results of cDNA complement consensus visible portion of view
*/
- protected AlignmentI alignment;
+ protected Hashtable[] hcomplementConsensus;
+
+ /**
+ * results of secondary structure base pair consensus for visible portion of
+ * view
+ */
+ protected Hashtable[] hStrucConsensus;
+
+ protected Conservation hconservation;
public AlignmentViewport(AlignmentI al)
{
return alignment.getGapCharacter();
}
- protected String sequenceSetID;
-
- /**
- * probably unused indicator that view is of a dataset rather than an
- * alignment
- */
- protected boolean isDataset = false;
-
public void setDataset(boolean b)
{
isDataset = b;
return isDataset;
}
- private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
-
- protected ColumnSelection colSel = new ColumnSelection();
-
- public boolean autoCalculateConsensus = true;
-
- protected boolean autoCalculateStrucConsensus = true;
-
- protected boolean ignoreGapsInConsensusCalculation = false;
-
- protected ResidueShaderI residueShading = new ResidueShader();
-
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
{
return residueShading;
}
-
- protected AlignmentAnnotation consensus;
-
- protected AlignmentAnnotation complementConsensus;
-
- protected AlignmentAnnotation gapcounts;
-
- protected AlignmentAnnotation strucConsensus;
-
- protected AlignmentAnnotation conservation;
-
- protected AlignmentAnnotation quality;
-
- protected AlignmentAnnotation[] groupConsensus;
-
- protected AlignmentAnnotation[] groupConservation;
-
- /**
- * results of alignment consensus analysis for visible portion of view
- */
- protected ProfilesI hconsensus = null;
-
- /**
- * results of cDNA complement consensus visible portion of view
- */
- protected Hashtable[] hcomplementConsensus = null;
-
- /**
- * results of secondary structure base pair consensus for visible portion of
- * view
- */
- protected Hashtable[] hStrucConsensus = null;
-
- protected Conservation hconservation = null;
-
@Override
public void setConservation(Conservation cons)
{
}
@Override
- public void setSequenceConsensusHash(ProfilesI hconsensus)
+ public void setConsensusProfiles(ProfilesI hconsensus)
{
- this.hconsensus = hconsensus;
+ this.consensusProfiles = hconsensus;
}
@Override
}
@Override
- public ProfilesI getSequenceConsensusHash()
+ public ProfilesI getConsensusProfiles()
{
- return hconsensus;
+ return consensusProfiles;
+ }
+
+ @Override
+ public void setHmmProfiles(ProfilesI info)
+ {
+ hmmProfiles = info;
+ }
+
+ @Override
+ public ProfilesI getHmmProfiles()
+ {
+ return hmmProfiles;
}
@Override
}
@Override
- public AlignmentAnnotation getAlignmentGapAnnotation()
+ public AlignmentAnnotation getOccupancyAnnotation()
{
- return gapcounts;
+ return occupancy;
}
@Override
}
}
+ /**
+ * 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)
{
strucConsensus = null;
conservation = null;
quality = null;
- groupConsensus = null;
- groupConservation = null;
- hconsensus = null;
+ consensusProfiles = null;
hconservation = null;
hcomplementConsensus = null;
- gapcounts = null;
+ occupancy = null;
calculator = null;
residueShading = null; // may hold a reference to Consensus
changeSupport = null;
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;
ignoreGapsInConsensusCalculation);
}
}
+ }
+ public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
+ {
+ boolean was = ignoreBelowBackGroundFrequencyCalculation;
+ ignoreBelowBackGroundFrequencyCalculation = b;
+ if (ap != null && was != b)
+ {
+ updateInformation(ap);
+ }
+ }
+
+ public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap)
+ {
+ boolean was = infoLetterHeight;
+ infoLetterHeight = b;
+ if (ap != null && was != b)
+ {
+ updateInformation(ap);
+ }
}
private long sgrouphash = -1, colselhash = -1;
return ignoreGapsInConsensusCalculation;
}
+ @Override
+ public boolean isIgnoreBelowBackground()
+ {
+ return ignoreBelowBackGroundFrequencyCalculation;
+ }
+
+ @Override
+ public boolean isInfoLetterHeight()
+ {
+ return infoLetterHeight;
+ }
+
// property change stuff
// JBPNote Prolly only need this in the applet version.
private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
{
updateConsensus(ap);
}
- if (hconsensus != null && autoCalculateConsensus)
+ if (consensusProfiles != null && autoCalculateConsensus)
{
updateConservation(ap);
}
{
updateStrucConsensus(ap);
}
+ // initInformation();
+ updateInformation(ap);
// Reset endRes of groups if beyond alignment width
int alWidth = alignment.getWidth();
{
rs.alignmentChanged(alignment, hiddenRepSequences);
- rs.setConsensus(hconsensus);
+ rs.setConsensus(consensusProfiles);
if (rs.conservationApplied())
{
rs.setConservation(Conservation.calculateConservation("All",
// depending on if the user wants to see the annotation or not in a
// specific alignment
- if (hconsensus == null && !isDataset)
+ if (consensusProfiles == null && !isDataset)
{
if (!alignment.isNucleotide())
{
MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
- initGapCounts();
+
+ initOccupancy();
initComplementConsensus();
}
// these should be extracted from the view model - style and settings for
// derived annotation
- private void initGapCounts()
+ private void initOccupancy()
{
if (showOccupancy)
{
- gapcounts = new AlignmentAnnotation("Occupancy",
+ occupancy = new AlignmentAnnotation("Occupancy",
MessageManager.getString("label.occupancy_descr"),
new Annotation[1], 0f, alignment.getHeight(),
AlignmentAnnotation.BAR_GRAPH);
- gapcounts.hasText = true;
- gapcounts.autoCalculated = true;
- gapcounts.scaleColLabel = true;
- gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+ occupancy.hasText = true;
+ occupancy.autoCalculated = true;
+ occupancy.scaleColLabel = true;
+ occupancy.graph = AlignmentAnnotation.BAR_GRAPH;
- alignment.addAnnotation(gapcounts);
+ alignment.addAnnotation(occupancy);
}
}
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)
{
return sq;
}
+ public boolean hasReferenceAnnotation()
+ {
+ AlignmentAnnotation[] annots = this.alignment.getAlignmentAnnotation();
+ for (AlignmentAnnotation annot : annots)
+ {
+ if ("RF".equals(annot.label) || annot.label.contains("Reference"))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
@Override
public void setCurrentTree(TreeModel tree)
{
.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))
try
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- AlignmentAnnotation gap = getGapAnnotation();
+ AlignmentAnnotation gap = getOccupancyAnnotation();
if ((consensus == null && gap == null) || calcMan.isPending(this))
{
calcMan.workerComplete(this);
{
AlignmentAnnotation consensus = getConsensusAnnotation();
consensus.annotations = new Annotation[aWidth];
- AlignmentAnnotation gap = getGapAnnotation();
+ AlignmentAnnotation gap = getOccupancyAnnotation();
if (gap != null)
{
gap.annotations = new Annotation[aWidth];
ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
true);
- alignViewport.setSequenceConsensusHash(hconsensus);
+ alignViewport.setConsensusProfiles(hconsensus);
setColourSchemeConsensus(hconsensus);
}
*
* @return
*/
- protected AlignmentAnnotation getGapAnnotation()
+ protected AlignmentAnnotation getOccupancyAnnotation()
{
- return alignViewport.getAlignmentGapAnnotation();
+ return alignViewport.getOccupancyAnnotation();
}
/**
&& hconsensus != null)
{
deriveConsensus(consensus, hconsensus);
- AlignmentAnnotation gap = getGapAnnotation();
- if (gap != null)
+ AlignmentAnnotation occupancy = getOccupancyAnnotation();
+ if (occupancy != null)
{
- deriveGap(gap, hconsensus);
+ deriveOccupancy(occupancy, hconsensus);
}
}
}
protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
ProfilesI hconsensus)
{
-
long nseq = getSequences().length;
AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
* @param hconsensus
* the computed consensus data
*/
- protected void deriveGap(AlignmentAnnotation gapAnnotation,
+ protected void deriveOccupancy(AlignmentAnnotation gapAnnotation,
ProfilesI hconsensus)
{
long nseq = getSequences().length;
- AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+ AAFrequency.completeOccupancyAnnot(gapAnnotation, hconsensus,
hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
nseq);
}
protected Object getViewportConsensus()
{
// TODO convert ComplementConsensusThread to use Profile
- return alignViewport.getSequenceConsensusHash();
+ return alignViewport.getConsensusProfiles();
}
}
--- /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.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
+import jalview.util.MessageManager;
+
+import java.util.List;
+
+/**
+ * This class calculates HMM Information Content annotations, based on any HMM
+ * consensus sequences and their HMM models. HMM consensus sequences may be
+ * present for the whole alignment, or subgroups of it.
+ *
+ */
+public class InformationThread extends AlignCalcWorker
+{
+ public static final String HMM_CALC_ID = "HMM";
+
+ private float max = 0f;
+
+ /**
+ * Constructor
+ *
+ * @param alignViewport
+ * @param alignPanel
+ */
+ public InformationThread(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ /**
+ * Recomputes Information annotations for any HMM consensus sequences (for
+ * alignment and/or groups)
+ */
+ @Override
+ public void run()
+ {
+ if (calcMan.isPending(this))
+ {
+ return;
+ }
+ calcMan.notifyStart(this);
+ // long started = System.currentTimeMillis();
+
+ try
+ {
+ if (calcMan.isPending(this))
+ {
+ // another instance of this is waiting to run
+ calcMan.workerComplete(this);
+ return;
+ }
+ while (!calcMan.notifyWorking(this))
+ {
+ // another thread in progress, wait my turn
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false, false);
+ }
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ if (alignViewport.isClosed())
+ {
+ abortAndDestroy();
+ return;
+ }
+ AlignmentI alignment = alignViewport.getAlignment();
+
+ int aWidth = alignment == null ? -1 : alignment.getWidth();
+
+ if (aWidth < 0)
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+
+ eraseAnnotations(alignment);
+ computeProfiles(alignment);
+ updateResultAnnotation(true);
+
+ if (ap != null)
+ {
+ ap.adjustAnnotationHeight();
+ ap.paintAlignment(true, true);
+ }
+ } catch (OutOfMemoryError error)
+ {
+ calcMan.disableWorker(this);
+ ap.raiseOOMWarning("calculating information", error);
+ } finally
+ {
+ calcMan.workerComplete(this);
+ }
+ }
+
+ /**
+ * Deletes any existing information annotations. These are sequence-related
+ * annotations which relate to HMM consensus sequences for either the
+ * alignment or a subgroup.
+ *
+ * @param alignment
+ */
+ protected void eraseAnnotations(AlignmentI alignment)
+ {
+ Iterable<AlignmentAnnotation> anns = alignment
+ .findAnnotation(HMM_CALC_ID);
+ for (AlignmentAnnotation ann : anns)
+ {
+ alignment.deleteAnnotation(ann);
+ }
+ }
+
+ /**
+ * Computes HMM profiles for any HMM consensus sequences (for alignment or
+ * subgroups)
+ *
+ * @param alignment
+ */
+ protected void computeProfiles(AlignmentI alignment)
+ {
+ int width = alignment.getWidth();
+
+ /*
+ * alignment HMM profile
+ */
+ SequenceI seq = alignment.getHmmConsensus();
+ if (seq != null)
+ {
+ HiddenMarkovModel hmm = seq.getHMM();
+ ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
+ 0, width, true, alignViewport.isIgnoreBelowBackground(),
+ alignViewport.isInfoLetterHeight());
+ alignViewport.setHmmProfiles(hmmProfiles);
+ // setColourSchemeInformation(hmmProfiles);
+ }
+
+ /*
+ * group HMM profiles
+ */
+ List<SequenceGroup> groups = alignment.getGroups();
+ for (SequenceGroup group : groups)
+ {
+ seq = group.getHmmConsensus();
+ if (seq != null)
+ {
+ HiddenMarkovModel hmm = seq.getHMM();
+ ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
+ 0, width, true, group.isIgnoreBelowBackground(),
+ group.isUseInfoLetterHeight());
+ group.setHmmProfiles(hmmProfiles);
+ // setColourSchemeInformation(hmmProfiles);
+ }
+ }
+ }
+
+ /**
+ * 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 Gap annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getGapAnnotation()
+ {
+ return alignViewport.getOccupancyAnnotation();
+ }
+
+ /**
+ * Updates the information annotation from the sequence profile data using
+ * current visualisation settings
+ */
+ @Override
+ public void updateAnnotation()
+ {
+ updateResultAnnotation(false);
+ }
+
+ /**
+ * Constructs Information Content annotation for any HMM consensus sequences
+ * (for alignment or groups), and adds the annotation to the sequence and the
+ * alignment
+ *
+ * @param immediate
+ */
+ public void updateResultAnnotation(boolean immediate)
+ {
+ AlignmentI alignment = alignViewport.getAlignment();
+
+ /*
+ * annotation for alignment HMM consensus if present
+ */
+ SequenceI hmmSeq = alignment.getHmmConsensus();
+ ProfilesI profile = alignViewport.getHmmProfiles();
+ AlignmentAnnotation ann = makeInformationAnnotation(hmmSeq, profile);
+ if (ann != null)
+ {
+ alignment.addAnnotation(ann);
+ }
+
+ /*
+ * annotation for group HMM consensus if present
+ */
+ for (SequenceGroup group : alignment.getGroups())
+ {
+ hmmSeq = group.getHmmConsensus();
+ ProfilesI profiles = group.getHmmProfiles();
+ ann = makeInformationAnnotation(hmmSeq, profiles);
+ if (ann != null)
+ {
+ ann.groupRef = group;
+ alignment.addAnnotation(ann);
+ }
+ }
+ }
+
+ /**
+ * Constructs an HMM Profile information content annotation for a sequence
+ *
+ * @param seq
+ * @param profile
+ * @return
+ */
+ protected AlignmentAnnotation makeInformationAnnotation(SequenceI seq,
+ ProfilesI profile)
+ {
+ if (seq == null || profile == null)
+ {
+ return null;
+ }
+
+ AlignmentI alignment = alignViewport.getAlignment();
+ int aWidth = alignment == null ? 0 : alignment.getWidth();
+ AlignmentAnnotation ann = new AlignmentAnnotation(seq.getName(),
+ MessageManager.getString("label.information_description"),
+ new Annotation[aWidth], 0f, 6.52f,
+ AlignmentAnnotation.BAR_GRAPH);
+ ann.hasText = true;
+ ann.autoCalculated = false;
+ ann.sequenceRef = seq;
+ ann.setCalcId(InformationThread.HMM_CALC_ID);
+ seq.addAlignmentAnnotation(ann);
+
+ long nseq = getSequences().length;
+ max = AAFrequency.completeInformation(ann, profile,
+ profile.getStartColumn(), profile.getEndColumn() + 1, nseq,
+ max);
+
+ return ann;
+ }
+
+ /**
+ * 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;
+ max = AAFrequency.completeInformation(informationAnnotation,
+ hinformation, hinformation.getStartColumn(),
+ hinformation.getEndColumn() + 1, nseq, max);
+ }
+}
/**
* 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;
public enum ValueType
{
- Integer, Float, String
+ Integer, Float, String, Double
};
ValueType getType();
--- /dev/null
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+
+/**
+ *
+ * @author TZVanaalten
+ *
+ */
+public class DoubleParameter extends Option implements ParameterI
+{
+ Double defval;
+
+ Double min, max;
+
+ @Override
+ public ValueConstrainI getValidValue()
+ {
+ return new ValueConstrainI()
+ {
+
+ @Override
+ public ValueType getType()
+ {
+ return ValueType.Double;
+ }
+
+ @Override
+ public Number getMin()
+ {
+ if (min < max)
+ {
+ return min;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ public Number getMax()
+ {
+ if (min < max)
+ {
+ return max;
+ }
+ else
+ {
+ return null;
+ }
+ }
+ };
+ }
+
+ public DoubleParameter(DoubleParameter parm)
+ {
+ super(parm);
+ max = parm.max;
+ min = parm.min;
+ }
+
+ public DoubleParameter(String name, String description, boolean required,
+ Double defValue, Double min, Double max)
+ {
+ super(name, description, required, String.valueOf(defValue), null, null,
+ null);
+ defval = defValue;
+ this.min = min;
+ this.max = max;
+ }
+
+ public DoubleParameter(String name, String description, boolean required,
+ Double defValue, Double value, Double min, Double max)
+ {
+ super(name, description, required, String.valueOf(defValue),
+ String.valueOf(value), null, null);
+ defval = defValue;
+ this.min = min;
+ this.max = max;
+ }
+
+ @Override
+ public DoubleParameter copy()
+ {
+ return new DoubleParameter(this);
+ }
+}
--- /dev/null
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+
+/**
+ *
+ * @author TZVanaalten
+ *
+ */
+public class LogarithmicParameter extends Option implements ParameterI
+{
+ Double defval;
+
+ Double min, max;
+
+ Double base;
+
+ @Override
+ public ValueConstrainI getValidValue()
+ {
+ return new ValueConstrainI()
+ {
+
+ @Override
+ public ValueType getType()
+ {
+ return ValueType.Double;
+ }
+
+ @Override
+ public Number getMin()
+ {
+ if (min < max)
+ {
+ return min;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ public Number getMax()
+ {
+ if (min < max)
+ {
+ return max;
+ }
+ else
+ {
+ return null;
+ }
+ }
+ };
+ }
+
+ public LogarithmicParameter(LogarithmicParameter parm)
+ {
+ super(parm);
+ max = parm.max;
+ min = parm.min;
+ base = parm.base;
+ }
+
+ public LogarithmicParameter(String name, String description,
+ boolean required, Double defValue, Double min, Double max,
+ Double base)
+ {
+ super(name, description, required, String.valueOf(defValue), null, null,
+ null);
+ defval = defValue;
+ this.min = min * 1000000;
+ this.max = max * 1000000;
+ this.base = base;
+ }
+
+ public LogarithmicParameter(String name, String description,
+ boolean required, Double defValue, Double value, Double min,
+ Double max, Double base)
+ {
+ super(name, description, required, String.valueOf(defValue),
+ String.valueOf(value), null, null);
+ defval = defValue;
+ this.min = min * 1000000;
+ this.max = max * 1000000;
+ this.base = base;
+ }
+
+ @Override
+ public LogarithmicParameter copy()
+ {
+ return new LogarithmicParameter(this);
+ }
+
+ public Double getBase()
+ {
+ return base;
+ }
+}
--- /dev/null
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+
+import java.net.URL;
+import java.util.List;
+
+public class StringParameter extends Option implements ParameterI
+{
+
+ @Override
+ public URL getFurtherDetails()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public boolean isRequired()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public String getDescription()
+ {
+ // TODO Auto-generated method stub
+ return description;
+ }
+
+ @Override
+ public List<String> getPossibleValues()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getName()
+ {
+ // TODO Auto-generated method stub
+ return name;
+ }
+
+ @Override
+ public String getValue()
+ {
+ // TODO Auto-generated method stub
+ return value;
+ }
+
+ @Override
+ public void setValue(String selectedItem)
+ {
+ value = selectedItem;
+
+ }
+
+ @Override
+ public ValueConstrainI getValidValue()
+ {
+ // TODO Auto-generated method stub
+ return new StringValueConstrain();
+ }
+
+ @Override
+ public ParameterI copy()
+ {
+ return new StringParameter(this);
+ }
+
+ private class StringValueConstrain implements ValueConstrainI
+ {
+
+ @Override
+ public ValueType getType()
+ {
+ return ValueType.String;
+ }
+
+ @Override
+ public Number getMax()
+ {
+ return null;
+ }
+
+ @Override
+ public Number getMin()
+ {
+ return null;
+ }
+
+ }
+
+ public StringParameter(StringParameter parm)
+ {
+ this.name = parm.name;
+ this.defvalue = parm.defvalue;
+ }
+
+ public StringParameter(String name, String description, boolean required,
+ String defValue)
+ {
+ super(name, description, required, String.valueOf(defValue), null, null,
+ null);
+ this.defvalue = defValue;
+ }
+
+ public StringParameter(String name, String description, boolean required,
+ String defValue, String value)
+ {
+ super(name, description, required, String.valueOf(defValue),
+ String.valueOf(value), null, null);
+ this.defvalue = defValue;
+ }
+}
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()
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @BeforeClass(alwaysRun = true)
+ public void setUp() throws IOException, MalformedURLException
+ {
+ /*
+ * load a dna (ACGT) HMM file to a HiddenMarkovModel
+ */
+ HMMFile hmmFile = new HMMFile(new FileParse(
+ "test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE));
+ hmm = hmmFile.getHMM();
+ }
+
@Test(groups = { "Functional" })
public void testCalculate_noProfile()
{
assertEquals("T 75%", ann.description);
assertEquals("T", ann.displayCharacter);
}
+
+ @Test(groups = { "Functional" })
+ public void testExtractHMMProfile()
+ throws MalformedURLException, IOException
+ {
+ int[] expected = { 0, 4, 100, 'T', 71, 'C', 12, 'G', 9, 'A', 9 };
+ int[] actual = AAFrequency.extractHMMProfile(hmm, 17, false, 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, false);
+ 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, false));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetAnalogueCount()
+ {
+ /*
+ * 'T' in column 0 has emission probability 0.7859, scales to 7859
+ */
+ int count = AAFrequency.getAnalogueCount(hmm, 0, 'T', false, false);
+ assertEquals(7859, count);
+
+ /*
+ * same with 'use info height': value is multiplied by log ratio
+ * log(value / background) / log(2) = log(0.7859/0.25)/0.693
+ * = log(3.1)/0.693 = 1.145/0.693 = 1.66
+ * so value becomes 1.2987 and scales up to 12987
+ */
+ count = AAFrequency.getAnalogueCount(hmm, 0, 'T', false, true);
+ assertEquals(12987, count);
+
+ /*
+ * 'G' in column 20 has emission probability 0.75457, scales to 7546
+ */
+ count = AAFrequency.getAnalogueCount(hmm, 20, 'G', false, false);
+ assertEquals(7546, count);
+
+ /*
+ * 'G' in column 1077 has emission probability 0.0533, here
+ * ignored (set to 0) since below background of 0.25
+ */
+ count = AAFrequency.getAnalogueCount(hmm, 1077, 'G', true, false);
+ assertEquals(0, count);
+ }
+
+ @Test(groups = { "Functional" })
+ 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, 1, 1f);
+ 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;
+ }
+
}
"Temperature Factor", null, false, seq, null);
assertNotNull(ala);
assertEquals(seq, ala.sequenceRef);
- assertEquals("", ala.calcId);
+ assertEquals("", ala.getCalcId());
}
@Test(groups = "Functional")
--- /dev/null
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.schemes.ResidueProperties;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HiddenMarkovModelTest {
+
+ HiddenMarkovModel hmm;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp() throws MalformedURLException, IOException
+ {
+ /*
+ * load hmm model of a Kinase domain to a HiddenMarkovModel
+ */
+ HMMFile file = new HMMFile(new FileParse(
+ "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
+ hmm = file.getHMM();
+ }
+
+ @Test(groups = "Functional")
+ public void testGetMatchEmissionProbabilities()
+ throws MalformedURLException, IOException
+ {
+ /*
+ * raw value in file is 3.67403
+ * saved as probability e^-X = 0.05259
+ */
+ double mep = hmm.getMatchEmissionProbability(0, 'R');
+ assertEquals(mep, 0.02537400637, 0.0001d);
+ assertEquals(mep, Math.pow(Math.E, -3.67403), 0.0001d);
+
+ mep = hmm.getMatchEmissionProbability(19, 'W');
+ assertEquals(mep, 0.00588228492, 0.0001d);
+ assertEquals(mep, Math.pow(Math.E, -5.13581), 0.0001d);
+
+ // column 160 is a gapped region of the model
+ mep = hmm.getMatchEmissionProbability(160, 'G');
+ assertEquals(mep, 0D, 0.0001d);
+
+ mep = hmm.getMatchEmissionProbability(475, 'A');
+ assertEquals(mep, 0.04995163708, 0.0001d);
+ assertEquals(mep, Math.pow(Math.E, -2.99670), 0.0001d);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetInsertEmissionProbabilities()
+ {
+ double iep = hmm.getInsertEmissionProbability(2, 'A');
+ assertEquals(iep, Math.pow(Math.E, -2.68618), 0.0001d);
+ // symbol is not case-sensitive
+ assertEquals(iep, hmm.getInsertEmissionProbability(2, 'a'));
+
+ iep = hmm.getInsertEmissionProbability(5, 'T');
+ assertEquals(iep, Math.pow(Math.E, -2.77519), 0.0001d);
+
+ // column 161 is gapped in the hmm
+ iep = hmm.getInsertEmissionProbability(161, 'K');
+ assertEquals(iep, 0D, 0.0001d);
+
+ iep = hmm.getInsertEmissionProbability(472, 'L');
+ assertEquals(iep, Math.pow(Math.E, -2.69355), 0.0001d);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetStateTransitionProbabilities()
+ {
+ // * in model file treated as negative infinity
+ double stp = hmm.getStateTransitionProbability(475,
+ HiddenMarkovModel.MATCHTODELETE);
+ assertEquals(stp, Double.NEGATIVE_INFINITY);
+
+ // file value is 5.01631, saved as e^-5.01631
+ stp = hmm.getStateTransitionProbability(8,
+ HiddenMarkovModel.MATCHTOINSERT);
+ assertEquals(stp, Math.pow(Math.E, -5.01631), 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(36,
+ HiddenMarkovModel.MATCHTODELETE);
+ assertEquals(stp, Math.pow(Math.E, -5.73865), 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(22,
+ HiddenMarkovModel.INSERTTOMATCH);
+ assertEquals(stp, Math.pow(Math.E, -0.61958), 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(80,
+ HiddenMarkovModel.INSERTTOINSERT);
+ assertEquals(stp, Math.pow(Math.E, -0.77255), 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(475,
+ HiddenMarkovModel.DELETETOMATCH);
+ assertEquals(stp, 1D, 0.0001D);
+
+ stp = hmm.getStateTransitionProbability(218,
+ HiddenMarkovModel.DELETETODELETE);
+ assertEquals(stp, Math.pow(Math.E, -0.95510), 0.0001D);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetConsensusAtAlignColumn()
+ {
+ assertEquals(hmm.getConsensusAtAlignColumn(10), 's');
+ assertEquals(hmm.getConsensusAtAlignColumn(50), 'k');
+ hmm.setProperty(HMMFile.CONSENSUS_RESIDUE, "no");
+ assertEquals(hmm.getConsensusAtAlignColumn(100), 'l');
+ assertEquals(hmm.getConsensusAtAlignColumn(400), 'k');
+ }
+
+ @Test(groups = "Functional")
+ 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------");
+ }
+
+ /**
+ * A rather pointless test that reproduces the code implemented and asserts
+ * the result is the same...
+ */
+ @Test(groups = "Functional")
+ public void testGetInformationContent()
+ {
+ /*
+ * information measure is sum over all symbols of
+ * emissionProb * log(emissionProb / background) / log(2)
+ */
+ Map<Character, Float> uniprotFreqs = ResidueProperties.backgroundFrequencies
+ .get("amino");
+ int col = 4;
+ float expected = 0f;
+ for (char aa : hmm.getSymbols().toCharArray())
+ {
+ double mep = hmm.getMatchEmissionProbability(col, aa);
+ float background = uniprotFreqs.get(aa);
+ expected += mep * Math.log(mep / background);
+ }
+ expected /= Math.log(2D);
+
+ float actual = hmm.getInformationContent(col);
+ assertEquals(actual, expected, 0.0001d);
+ }
+}
import jalview.datamodel.ResidueCount.SymbolCounts;
import jalview.gui.JvOptionPane;
+import java.util.Arrays;
+
import org.junit.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
assertEquals(rc.getCount('N'), 1);
assertEquals(rc.getCount('?'), 0);
assertEquals(rc.getCount('-'), 0);
+ assertEquals(rc.getTotalResidueCount(), 11);
assertFalse(rc.isCountingInts());
assertFalse(rc.isUsingOtherData());
assertEquals(rc.getCount(' '), 4);
assertEquals(rc.getCount('-'), 4);
assertEquals(rc.getCount('.'), 4);
+ assertEquals(rc.getTotalResidueCount(), 0);
assertFalse(rc.isUsingOtherData());
assertFalse(rc.isCountingInts());
}
assertEquals(rc.getCount('m'), 13);
assertEquals(rc.getCount('G'), 0);
assertEquals(rc.getCount('-'), 0);
+ assertEquals(rc.getTotalResidueCount(), 27);
assertFalse(rc.isCountingInts());
assertFalse(rc.isUsingOtherData());
assertEquals(rc.getCount('?'), 6);
assertEquals(rc.getCount('!'), 7);
}
+
+ @Test(groups = "Functional")
+ public void testConstructor_forSequences()
+ {
+ SequenceI seq1 = new Sequence("seq1", "abcde--. FCD");
+ SequenceI seq2 = new Sequence("seq2", "ab.kKqBd-.");
+ ResidueCount rc = new ResidueCount(Arrays.asList(seq1, seq2));
+
+ assertEquals(rc.getGapCount(), 7);
+ assertEquals(rc.getTotalResidueCount(), 15); // excludes gaps
+ assertEquals(rc.getCount('a'), 2);
+ assertEquals(rc.getCount('A'), 2);
+ assertEquals(rc.getCount('B'), 3);
+ assertEquals(rc.getCount('c'), 2);
+ assertEquals(rc.getCount('D'), 3);
+ assertEquals(rc.getCount('f'), 1);
+ assertEquals(rc.getCount('K'), 2);
+ assertEquals(rc.getCount('Q'), 1);
+ }
}
import java.awt.Color;
import java.util.Collections;
-import junit.extensions.PA;
-
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SequenceGroupTest
{
@Test(groups={"Functional"})
sg.setDisplayBoxes(false);
sg.setDisplayText(false);
sg.setColourText(true);
- sg.isDefined = true;
+ PA.setValue(sg, "isDefined", true);
sg.setShowNonconserved(true);
sg.setOutlineColour(Color.red);
sg.setIdColour(Color.blue);
assertEquals(sg2.thresholdTextColour, sg.thresholdTextColour);
assertEquals(sg2.textColour, sg.textColour);
assertEquals(sg2.textColour2, sg.textColour2);
- assertEquals(sg2.getIgnoreGapsConsensus(), sg.getIgnoreGapsConsensus());
+ assertEquals(sg2.isIgnoreGapsConsensus(), sg.isIgnoreGapsConsensus());
assertEquals(sg2.isShowSequenceLogo(), sg.isShowSequenceLogo());
assertEquals(sg2.isNormaliseSequenceLogo(),
sg.isNormaliseSequenceLogo());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
AlignViewport av = af.getViewport();
- Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
+ Assert.assertNull(av.getOccupancyAnnotation(), "Preference did not disable occupancy row.");
int c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
null, "Occupancy"))
af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
av = af.getViewport();
- Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
+ Assert.assertNotNull(av.getOccupancyAnnotation(), "Preference did not enable occupancy row.");
c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
- null, av.getAlignmentGapAnnotation().label))
+ null, av.getOccupancyAnnotation().label))
{
c++;
}
--- /dev/null
+package jalview.hmmer;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.HMMFile;
+import jalview.ws.params.ArgumentI;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.ArrayList;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HMMERTest {
+
+ AlignFrame frame;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpBeforeClass() throws Exception
+ {
+ Jalview.main(
+ new String[]
+ { "-noquestionnaire", "-nonews", "-props",
+ "test/jalview/hmmer/testProps.jvprops", "-open",
+ "examples/uniref50.fa" });
+ // FastaFile file = null;
+ // file = new FastaFile(
+ // new FileParse("examples/uniref50.fa", DataSourceType.FILE));
+ // SequenceI[] seqs = file.getSeqsAsArray();
+ // AlignmentI al = new Alignment(seqs);
+ // frame = new AlignFrame(al, 150, 20);
+ frame = Desktop.getAlignFrames()[0];
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ /**
+ * Test with a dependency on locally installed hmmbuild binaries
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "External")
+ public void testHMMBuildThenHMMAlign()
+ throws MalformedURLException, IOException
+ {
+ /*
+ * run hmmbuild - note the side-effect of selecting the HMM
+ * sequence that gets added to the alignment
+ */
+ testHMMBuild();
+ HiddenMarkovModel hmm = frame.getSelectedHMM();
+ assertNotNull(hmm);
+
+ /*
+ * now run hmmalign - with respect to the select HMM profile
+ */
+ testHMMAlign();
+ }
+
+ public void testHMMBuild()
+ {
+ HMMBuild builder = new HMMBuild(frame,
+ new ArrayList<ArgumentI>());
+ builder.run();
+
+ SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
+ HiddenMarkovModel hmm = seq.getHMM();
+ assertNotNull(hmm);
+
+ assertEquals(hmm.getLength(), 148);
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertEquals(hmm.getName(), "Alignment_HMM");
+ assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+ "0.648193");
+ assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
+ }
+
+ public void testHMMAlign()
+ {
+ HMMAlign thread = new HMMAlign(frame,
+ new ArrayList<ArgumentI>());
+ thread.run();
+
+ AlignFrame[] alignFrames = Desktop.getAlignFrames();
+ if (alignFrames == null)
+ {
+ fail("No align frame loaded");
+ }
+
+ /*
+ * now have the original align frame, and another for realigned sequences
+ */
+ assertEquals(alignFrames.length, 2);
+ AlignmentI original = alignFrames[0].getViewport().getAlignment();
+ assertNotNull(original);
+ AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
+ assertNotNull(realigned);
+ assertNotNull(original.getHmmConsensus());
+ assertNotNull(realigned.getHmmConsensus());
+
+ SequenceI ferCapan = original.findName("FER_CAPAN");
+ assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
+
+ SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
+ assertTrue(ferCapanRealigned.getSequenceAsString()
+ .startsWith("-------m-A----SVSAT"));
+ }
+}
+
--- /dev/null
+#---JalviewX Properties File---
+#Fri Apr 25 09:54:25 BST 2014
+SCREEN_Y=768
+SCREEN_X=936
+SHOW_WSDISCOVERY_ERRORS=true
+LATEST_VERSION=2.8.0b1
+SHOW_CONSERVATION=true
+JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
+JAVA_CONSOLE_SCREEN_WIDTH=450
+LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
+ID_ITALICS=true
+SORT_ALIGNMENT=No sort
+SHOW_IDENTITY=true
+WSMENU_BYHOST=false
+SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
+SHOW_FULLSCREEN=false
+RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
+FONT_NAME=SansSerif
+BLC_JVSUFFIX=true
+VERSION_CHECK=false
+YEAR=2011
+SHOW_DBREFS_TOOLTIP=true
+MSF_JVSUFFIX=true
+SCREENGEOMETRY_HEIGHT=1600
+JAVA_CONSOLE_SCREEN_Y=475
+JAVA_CONSOLE_SCREEN_X=830
+PFAM_JVSUFFIX=true
+PIR_JVSUFFIX=true
+STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
+JAVA_CONSOLE_SCREEN_HEIGHT=162
+PIR_MODELLER=false
+GAP_SYMBOL=-
+SHOW_QUALITY=true
+SHOW_OCCUPANCY=true
+SHOW_GROUP_CONSERVATION=false
+SHOW_JWS2_SERVICES=true
+SHOW_NPFEATS_TOOLTIP=true
+FONT_STYLE=plain
+ANTI_ALIAS=false
+SORT_BY_TREE=false
+RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
+SHOW_GROUP_CONSENSUS=false
+SHOW_CONSENSUS_HISTOGRAM=true
+SHOW_OVERVIEW=false
+AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+FIGURE_AUTOIDWIDTH=false
+SCREEN_WIDTH=900
+ANNOTATIONCOLOUR_MIN=ffc800
+SHOW_STARTUP_FILE=false
+RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
+DEFAULT_FILE_FORMAT=FASTA
+SHOW_JAVA_CONSOLE=false
+VERSION=2.8b1
+FIGURE_USERIDWIDTH=
+WSMENU_BYTYPE=false
+DEFAULT_COLOUR=None
+NOQUESTIONNAIRES=true
+JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
+BUILD_DATE=01 November 2013
+PILEUP_JVSUFFIX=true
+SHOW_CONSENSUS_LOGO=false
+SCREENGEOMETRY_WIDTH=2560
+SHOW_ANNOTATIONS=true
+JALVIEW_RSS_WINDOW_SCREEN_Y=0
+USAGESTATS=false
+JALVIEW_RSS_WINDOW_SCREEN_X=0
+SHOW_UNCONSERVED=false
+SHOW_JVSUFFIX=true
+DAS_LOCAL_SOURCE=
+SCREEN_HEIGHT=650
+ANNOTATIONCOLOUR_MAX=ff0000
+AUTO_CALC_CONSENSUS=true
+FASTA_JVSUFFIX=true
+DAS_ACTIVE_SOURCE=uniprot\t
+JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
+PAD_GAPS=false
+CLUSTAL_JVSUFFIX=true
+SHOW_ENFIN_SERVICES=true
+FONT_SIZE=10
+RIGHT_ALIGN_IDS=false
+USE_PROXY=false
+WRAP_ALIGNMENT=false
+#DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+logs.Jalview.level=DEBUG
+HMMER_PATH=/Users/gmcarstairs/software/hmmer-3.1b2-macosx-intel/binaries
@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.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+
+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.Scanner;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import junit.extensions.PA;
+
+public class HMMFileTest {
+
+ HMMFile fn3;
+
+ HMMFile pKinase;
+
+ HMMFile made1;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp() throws IOException
+ {
+ fn3 = new HMMFile("test/jalview/io/test_fn3_hmm.txt",
+ DataSourceType.FILE);
+
+ pKinase = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+ DataSourceType.FILE);
+
+ made1 = new HMMFile("test/jalview/io/test_MADE1_hmm.txt",
+ DataSourceType.FILE);
+ }
+
+ @Test(groups = "Functional")
+ public void testParse() throws IOException
+ {
+ HiddenMarkovModel hmm = pKinase.getHMM();
+ assertEquals(hmm.getName(), "Pkinase");
+ assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER), "PF00069.17");
+ assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
+ "Protein kinase domain");
+ assertEquals(hmm.getLength(), 260);
+ assertNull(hmm.getProperty(HMMFile.MAX_LENGTH));
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertFalse(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
+ assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
+ assertEquals(hmm.getProperty(HMMFile.DATE), "Thu Jun 16 11:44:06 2011");
+ assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
+ assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "54");
+ assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+ "3.358521");
+ assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3106786190");
+ assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD),
+ "70.30 70.30");
+ assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "70.30 70.30");
+ assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "70.20 70.20");
+
+ assertEquals(hmm.getSymbols(), "ACDEFGHIKLMNPQRSTVWY");
+
+ 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 that Jalview can parse an HMM file even with a bunch of 'mandatory'
+ * fields missing (including no MAP annotation or // terminator line)
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testParse_minimalFile() throws IOException
+ {
+ /*
+ * ALPH is absent, alphabet inferred from HMM header line
+ * Optional COMPO line is absent
+ * first line after HMM is a guide line for readability
+ * next line is BEGIN node insert emissions
+ * next line is BEGIN node transitions
+ * next line is first sequence node match emissions 1.1 1.2 1.3
+ * next line is first sequence node insert emissions 1.4 1.5 1.6
+ * last line is first sequence node transitions
+ */
+ //@formatter:off
+ String hmmData =
+ "HMMER3\n" +
+ "HMM P M J\n" +
+ // both spec and parser require a line after the HMM line
+ " m->m m->i m->d i->m i->i d->m d->d\n" +
+ " 0.1 0.2 0.3\n" +
+ " 0.4 0.5 0.6 0.7 0.8 0.9 0.95\n" +
+ " 1 1.1 1.2 1.3 - - - - -\n" +
+ " 1.4 1.5 1.6\n" +
+ " 1.7 1.8 1.9 2.0 2.1 2.2 2.3\n" +
+ " 2 1.01 1.02 1.03 - - - - -\n" +
+ " 1.04 1.05 1.06\n" +
+ " 1.7 1.8 1.9 2.0 2.1 2.2 2.3\n";
+ //@formatter:on
+ HMMFile parser = new HMMFile(hmmData, DataSourceType.PASTE);
+ HiddenMarkovModel hmm = parser.getHMM();
+ assertNotNull(hmm);
+ assertEquals(hmm.getSymbols(), "PMJ");
+ assertEquals(hmm.getLength(), 0); // no LENG property :-(
+
+ // node 1 (implicitly mapped to column 0)
+ double prob = hmm.getMatchEmissionProbability(0, 'p');
+ assertEquals(prob, Math.pow(Math.E, -1.1));
+ prob = hmm.getInsertEmissionProbability(0, 'J');
+ assertEquals(prob, Math.pow(Math.E, -1.6));
+
+ // node 2 (implicitly mapped to column 1)
+ prob = hmm.getMatchEmissionProbability(1, 'M');
+ assertEquals(prob, Math.pow(Math.E, -1.02));
+ prob = hmm.getInsertEmissionProbability(1, 'm');
+ assertEquals(prob, Math.pow(Math.E, -1.05));
+ }
+
+ @Test(groups = "Functional")
+ public void testParseHeaderLines_amino() throws IOException
+ {
+ FileReader fr = new FileReader(
+ new File("test/jalview/io/test_fn3_hmm.txt"));
+ BufferedReader br = new BufferedReader(fr);
+ HiddenMarkovModel hmm = new HiddenMarkovModel();
+ HMMFile testee = new HMMFile();
+ PA.setValue(testee, "hmm", hmm);
+ testee.parseHeaderLines(br);
+ br.close();
+ fr.close();
+
+ assertEquals(hmm.getName(), "fn3");
+ assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER), "PF00041.13");
+ assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
+ "Fibronectin type III domain");
+ assertEquals(hmm.getProperty(HMMFile.LENGTH), "86");
+ assertNull(hmm.getProperty(HMMFile.MAX_LENGTH));
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertFalse(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
+ assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
+
+ assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
+ assertEquals(hmm.getProperty(HMMFile.DATE), "Fri Jun 20 08:22:31 2014");
+ assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
+ assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "106");
+ assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+ "11.415833");
+ assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3564431818");
+ assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD), "8.00 7.20");
+ assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "8.00 7.20");
+ assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "7.90 7.90");
+ assertEquals(hmm.getViterbi(), "-9.7737 0.71847");
+ assertEquals(hmm.getMSV(), "-9.4043 0.71847");
+ assertEquals(hmm.getForward(), "-3.8341 0.71847");
+ }
+
+ @Test(groups = "Functional")
+ public void testParseHeaderLines_dna() throws IOException
+ {
+ FileReader fr = new FileReader(
+ new File("test/jalview/io/test_MADE1_hmm.txt"));
+ BufferedReader br = new BufferedReader(fr);
+ HiddenMarkovModel hmm = new HiddenMarkovModel();
+ HMMFile testee = new HMMFile();
+ PA.setValue(testee, "hmm", hmm);
+ testee.parseHeaderLines(br);
+ br.close();
+ fr.close();
+
+ assertEquals(hmm.getName(), "MADE1");
+ assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER),
+ "DF0000629.2");
+ assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
+ "MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon");
+ assertEquals(hmm.getProperty(HMMFile.LENGTH), "80");
+ assertEquals(hmm.getProperty(HMMFile.MAX_LENGTH), "426");
+ assertEquals(hmm.getAlphabetType(), "DNA");
+ assertTrue(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
+ assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
+ assertFalse(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
+ assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
+ assertEquals(hmm.getProperty(HMMFile.DATE), "Tue Feb 19 20:33:41 2013");
+ assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
+ assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "1997");
+ assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES), "3.911818");
+ assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3015610723");
+ assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD),
+ "2.324 4.234");
+ assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "2.343 1.212");
+ assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "2.354 5.456");
+ assertEquals(hmm.getViterbi(), "-9.3632 0.71858");
+ assertEquals(hmm.getMSV(), "-8.5786 0.71858");
+ assertEquals(hmm.getForward(), "-3.4823 0.71858");
+ }
+
+ @Test(groups = "Functional")
+ 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);
+
+ double[] testList = HMMFile.parseDoubles(scanner1, 9);
+
+ for (int i = 0; i < 9; i++)
+ {
+ assertEquals(testList[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.parseDoubles(scanner2, 5);
+
+ for (int i = 0; i < 5; i++)
+ {
+ assertEquals(testList[i], filledArray.get(i), 0.001d);
+ }
+ }
+
+ @Test(groups = "Functional")
+ 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();
+ String line = null;
+ do
+ {
+ line = br.readLine(); // skip header lines up to HMM plus one
+ } while (!line.startsWith("HMM "));
+ 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(groups = "Functional")
+ public void testParseAnnotations()
+ {
+ HMMFile testFile = new HMMFile();
+ HiddenMarkovModel hmm = new HiddenMarkovModel();
+ PA.setValue(testFile, "hmm", hmm);
+ hmm.addNode(new HMMNode());
+
+ hmm.setProperty(HMMFile.CONSENSUS_RESIDUE, "yes");
+ hmm.setProperty(HMMFile.MAP, "yes");
+ hmm.setProperty(HMMFile.REFERENCE_ANNOTATION, "yes");
+ hmm.setProperty(HMMFile.CONSENSUS_STRUCTURE, "yes");
+ hmm.setProperty(HMMFile.MASKED_VALUE, "yes");
+ Scanner scanner = new Scanner("1345 t t t t");
+ HMMNode node = new HMMNode();
+ hmm.addNode(node);
+ testFile.parseAnnotations(scanner, node);
+
+ hmm.setProperty(HMMFile.CONSENSUS_RESIDUE, "yes");
+ hmm.setProperty(HMMFile.MAP, "no");
+ hmm.setProperty(HMMFile.REFERENCE_ANNOTATION, "yes");
+ hmm.setProperty(HMMFile.CONSENSUS_STRUCTURE, "no");
+ hmm.setProperty(HMMFile.MASKED_VALUE, "no");
+ Scanner scanner2 = new Scanner("- y x - -");
+ node = new HMMNode();
+ hmm.addNode(node);
+ testFile.parseAnnotations(scanner2, node);
+
+ 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');
+
+ scanner.close();
+ }
+
+ /**
+ * tests to see if file produced by the output matches the file from the input
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ 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++)
+ {
+ double[] list1;
+ double[] list2;
+
+ list1 = pKinaseHMM.getNode(i).getMatchEmissions();
+ list2 = pKinaseCloneHMM.getNode(i).getMatchEmissions();
+
+ assertEquals(list1, list2);
+
+ list1 = pKinaseHMM.getNode(i).getInsertEmissions();
+ list2 = pKinaseCloneHMM.getNode(i).getInsertEmissions();
+
+ assertEquals(list1, list2);
+
+ list1 = pKinaseHMM.getNode(i).getStateTransitions();
+ list2 = pKinaseCloneHMM.getNode(i).getStateTransitions();
+
+ assertEquals(list1, list2);
+
+ 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(groups = "Functional")
+ public void testAppendProperties() throws FileNotFoundException
+ {
+ StringBuilder sb = new StringBuilder();
+ fn3.appendProperties(sb);
+
+ Scanner testScanner = new Scanner(sb.toString());
+
+ 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(groups = "Functional")
+ public void testAppendModelAsString() throws FileNotFoundException
+ {
+ StringBuilder sb = new StringBuilder();
+ fn3.appendModelAsString(sb);
+ String string = sb.toString();
+
+ 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");
+ }
+
+ /**
+ * A helper method to find a token in the model string
+ *
+ * @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
+ */
+ private String findValue(int symbolIndex, int nodeIndex, int line,
+ String model)
+ {
+ String value = "";
+ Scanner scanner = new Scanner(model);
+ scanner.nextLine();
+ scanner.nextLine();
+
+ for (int lineIndex = 0; lineIndex < line - 1; lineIndex++)
+ {
+ scanner.nextLine();
+ }
+ for (int node = 0; node < nodeIndex; node++)
+ {
+ scanner.nextLine();
+ scanner.nextLine();
+ scanner.nextLine();
+ }
+
+ for (int symbol = 0; symbol < symbolIndex; symbol++)
+ {
+ value = scanner.next();
+ if ("COMPO".equals(value))
+ {
+ scanner.next();
+ }
+ else if (value.length() < 7)
+ {
+ scanner.next();
+ }
+ }
+ scanner.close();
+ return value;
+ }
+}
+
+ actualGrp.getColourText());
System.out.println(expectedGrp.getDisplayBoxes() + " | "
+ actualGrp.getDisplayBoxes());
- System.out.println(expectedGrp.getIgnoreGapsConsensus() + " | "
- + actualGrp.getIgnoreGapsConsensus());
+ System.out.println(expectedGrp.isIgnoreGapsConsensus() + " | "
+ + actualGrp.isIgnoreGapsConsensus());
System.out.println(expectedGrp.getSequences().size() + " | "
+ actualGrp.getSequences().size());
System.out.println(expectedGrp.getStartRes() + " | "
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getColourText() == actualGrp.getColourText()
&& expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
- && expectedGrp.getIgnoreGapsConsensus() == actualGrp
- .getIgnoreGapsConsensus()
+ && expectedGrp.isIgnoreGapsConsensus() == actualGrp
+ .isIgnoreGapsConsensus()
&& colourSchemeMatches
&& expectedGrp.getSequences().size() == actualGrp
.getSequences().size()
--- /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
+ 47 2.13251 2.88788 0.29508 2.50964 764 g x - -
+ 1.20891 1.55463 1.68206 1.19000
+ 0.06526 3.12574 3.94910 2.41448 0.09367 1.10396 0.40280
+ 48 2.23841 2.99164 0.25118 2.72900 792 g x - -
+ 1.26330 1.55339 1.52606 1.24355
+ 0.05464 3.34968 4.01313 2.78872 0.06347 1.15133 0.38012
+ 49 2.57533 0.32900 2.64632 2.01501 824 c x - -
+ 1.35118 1.39828 1.40141 1.39516
+ 0.04340 3.79297 3.91506 1.59549 0.22666 1.20075 0.35806
+ 50 0.46433 2.04127 2.23437 2.00605 833 a x - -
+ 1.23062 1.36903 1.62282 1.36182
+ 0.05764 3.31530 3.92762 2.28791 0.10700 1.07910 0.41536
+ 51 0.27513 2.77017 2.28518 2.57549 853 a x - -
+ 1.27958 1.58726 1.46109 1.25394
+ 0.05750 3.30072 3.96214 2.60776 0.07656 1.25708 0.33475
+ 52 0.20149 2.86434 2.84551 2.69770 883 a x - -
+ 1.23645 1.62259 1.71174 1.10368
+ 0.05756 3.26729 4.02702 2.54508 0.08172 1.27391 0.32814
+ 53 0.26982 2.65833 2.50477 2.46835 911 a x - -
+ 1.36005 1.50358 1.48100 1.22550
+ 0.06921 3.37553 3.42118 2.36646 0.09851 1.27560 0.32748
+ 54 0.40022 2.19284 2.22687 2.20396 934 a x - -
+ 1.12070 1.60472 1.53213 1.35895
+ 0.05523 3.36752 3.94966 2.42917 0.09224 0.84774 0.55928
+ 55 2.11356 0.46400 2.46442 1.79955 960 c x - -
+ 1.23932 1.35913 1.50478 1.46331
+ 0.05187 3.47055 3.94022 2.35854 0.09933 1.12102 0.39445
+ 56 1.85868 0.79440 2.22069 1.25971 983 c x - -
+ 1.21951 1.50212 1.51138 1.34185
+ 0.06404 3.29054 3.69705 1.75742 0.18933 1.18410 0.36532
+ 57 1.33272 2.32720 0.71452 1.90215 999 g x - -
+ 1.12229 1.49343 1.56653 1.42255
+ 0.04920 3.46654 4.08749 2.17995 0.11996 1.31769 0.31164
+ 58 2.48337 0.43652 2.46331 1.68683 1017 c x - -
+ 1.34704 1.55461 1.38112 1.28222
+ 0.04823 3.61532 3.90311 2.20911 0.11631 1.00864 0.45368
+ 59 0.41659 2.44509 1.93972 2.20507 1034 a x - -
+ 1.38198 1.38198 1.39194 1.38932
+ 0.03641 3.98130 4.06929 1.35873 0.29704 1.31330 0.31325
+ 60 0.41612 2.39160 1.97116 2.21075 1037 a x - -
+ 1.03649 1.46430 1.57421 1.57557
+ 0.04769 3.52580 4.06641 2.32461 0.10294 0.84329 0.56263
+ 61 2.66264 2.12302 2.82746 0.28581 1056 t x - -
+ 1.36925 1.39635 1.38930 1.39048
+ 0.04097 3.97400 3.84718 1.39433 0.28502 1.12205 0.39395
+ 62 2.26510 2.13196 2.42551 0.37231 1060 t x - -
+ 1.37965 1.39147 1.39147 1.38264
+ 0.04082 3.91610 3.90805 1.24613 0.33914 0.95192 0.48776
+ 63 0.41244 2.25761 2.16787 2.12907 1062 a x - -
+ 1.34515 1.41203 1.41203 1.37753
+ 0.04054 3.77835 4.08203 1.30483 0.31638 1.11819 0.39582
+ 64 2.51464 0.37905 2.62296 1.82008 1068 c x - -
+ 1.39543 1.38753 1.39233 1.37008
+ 0.03854 3.90584 4.03535 1.36573 0.29463 1.13682 0.38689
+ 65 2.16380 2.11332 2.18714 0.42765 1073 t x - -
+ 1.38764 1.38471 1.38519 1.38764
+ 0.03575 4.05376 4.03073 1.40080 0.28289 1.03825 0.43707
+ 66 2.79349 2.39141 2.87271 0.23478 1075 t x - -
+ 1.37227 1.39101 1.39101 1.39101
+ 0.03597 4.01447 4.05827 1.39017 0.28639 1.06429 0.42308
+ 67 2.82488 2.47749 2.93179 0.21887 1078 t x - -
+ 1.38141 1.39112 1.38915 1.38353
+ 0.03661 3.99477 4.04370 1.35958 0.29675 1.13439 0.38804
+ 68 2.77679 2.30433 2.90694 0.24425 1081 t x - -
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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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+ 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/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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+ 0.00227 6.08723 * 0.61958 0.77255 0.00000 *
+//
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.HMMFile;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.Test;
+
+public class HMMERAlignmentColourSchemeTest {
+
+ @Test(groups = "Functional")
+ public void testFindColour() throws MalformedURLException, IOException
+ {
+ HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+ DataSourceType.FILE);
+
+ /*
+ * alignment with 20 residues and background frequencies:
+ * A/a, S 3/20 = 0.15
+ * M, K 4/20 = 0.2
+ * V 2/20 = 0.1
+ * Q, R, L 1/20 = 0.05
+ * log(totalCount) = log(20) = 2.996
+ */
+ SequenceI seq1 = new Sequence("seq1", "AAMMMKKKVV");
+ SequenceI seq2 = new Sequence("seq2", "aAM-QKRSSSL");
+ AnnotatedCollectionI ac = new Alignment(new SequenceI[] { seq1, seq2 });
+ ColourSchemeI scheme = new HMMERAlignmentColourScheme(ac,
+ file.getHMM());
+
+ /*
+ * 'A' in column 1, node 2, match emission 2.77204
+ * e-2.77204 = 0.0625
+ * background frequency is 0.15
+ * ratio is < 1, log is negative, colour is Orange
+ */
+ Color actual = scheme.findColour('A', 1, null, null, 0);
+ assertEquals(actual, Color.ORANGE);
+
+ // gap is white
+ actual = scheme.findColour('-', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ actual = scheme.findColour(' ', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ actual = scheme.findColour('.', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+
+ /*
+ * 'L' in column 3, node 4, match emission 1.98342
+ * e-1.98342 = 0.1376
+ * background frequency is 0.05
+ * ratio is 2.752, log is 1.012
+ * colour is graduated 1.012/2.996 or 86/255 of the way from
+ * white(255, 255, 255) to blue(0, 0, 255)
+ */
+ actual = scheme.findColour('L', 3, null, null, 0);
+ assertEquals(actual, new Color(169, 169, 255));
+
+ /*
+ * invalid symbol is White
+ */
+ actual = scheme.findColour('X', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ }
+
+}
--- /dev/null
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.io.DataSourceType;
+import jalview.io.HMMFile;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.Test;
+
+public class HMMERColourSchemeTest {
+
+ @Test(groups = "Functional")
+ public void testFindColour() throws MalformedURLException, IOException
+ {
+ HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+ DataSourceType.FILE);
+
+ ColourSchemeI scheme = new HMMERColourScheme(file.getHMM());
+
+ /*
+ * 'A' in column 1, node 2, match emission 2.77204
+ * e-2.77204 = 0.0625
+ * background frequency is 0.0826
+ * ratio is 0.757, log is negative, colour is Orange
+ */
+ Color actual = scheme.findColour('A', 1, null, null, 0);
+ assertEquals(actual, Color.ORANGE);
+
+ // gap is white
+ actual = scheme.findColour('-', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ actual = scheme.findColour(' ', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+ actual = scheme.findColour('.', 2, null, null, 0);
+ assertEquals(actual, Color.WHITE);
+
+ /*
+ * 'Y' in column 4, node 5, match emission 4.41426
+ * e-4.41426 = 0.0121
+ * background frequency is 0.0292
+ * ratio is 0.414, log is negative, colour is Orange
+ */
+ actual = scheme.findColour('Y', 4, null, null, 0);
+ assertEquals(actual, Color.ORANGE);
+
+ /*
+ * 'M' in column 109, no matching node, colour is reddish
+ */
+ actual = scheme.findColour('M', 109, null, null, 0);
+ assertEquals(actual, new Color(230, 0, 0));
+
+ /*
+ * 'I' in column 6, node 7, match emission 1.33015
+ * e-1.33015 = 0.2644
+ * background frequency is 0.0593
+ * ratio is 4.459, log is 1.495
+ * colour is graduated 1.495/4.52 or 84/255 of the way from
+ * white(255, 255, 255) to blue(0, 0, 255)
+ */
+ actual = scheme.findColour('I', 6, null, null, 0);
+ assertEquals(actual, new Color(171, 171, 255));
+
+ /*
+ * 'V' in column 14, node 15, match emission 0.44769
+ * e-0.44769 = 0.6391
+ * background frequency is 0.0686
+ * ratio is 9.316, log is 2.232
+ * colour is graduated 2.232/4.52 or 126/255 of the way from
+ * white(255, 255, 255) to blue(0, 0, 255)
+ */
+ actual = scheme.findColour('V', 14, null, null, 0);
+ assertEquals(actual, new Color(129, 129, 255));
+
+ /*
+ * invalid symbol is White
+ */
+ actual = scheme.findColour('X', 2, 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.setProperty("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