1 package jalview.datamodel;
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5 /** Data structure to hold and manipulate a multiple sequence alignment
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7 public interface AlignmentI {
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9 public int getHeight() ;
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10 public int getWidth() ;
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11 public int getMaxIdLength() ;
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13 public boolean isAligned();
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15 public Vector getSequences();
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16 public SequenceI getSequenceAt(int i);
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18 public void addSequence(SequenceI seq) ;
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19 public void setSequenceAt(int i,SequenceI seq);
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21 public void deleteSequence(SequenceI s) ;
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22 public void deleteSequence(int i) ;
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24 public SequenceI[] getColumns(int start, int end) ;
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25 public SequenceI[] getColumns(int seq1, int seq2, int start, int end) ;
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27 public void deleteColumns(int start, int end) ;
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28 public void deleteColumns(int seq1, int seq2, int start, int end) ;
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30 public void insertColumns(SequenceI[] seqs, int pos) ;
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32 public SequenceI findName(String name) ;
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33 public SequenceI findbyDisplayId(String name);
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35 public int findIndex(SequenceI s) ;
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38 public void trimLeft(int i) ;
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39 public void trimRight(int i) ;
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41 public void removeGaps() ;
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42 public Vector removeRedundancy(float threshold, Vector sel) ;
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46 public SequenceGroup findGroup(int i) ;
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47 public SequenceGroup findGroup(SequenceI s) ;
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48 public SequenceGroup [] findAllGroups(SequenceI s);
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49 public void addToGroup(SequenceGroup g, SequenceI s) ;
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50 public void removeFromGroup(SequenceGroup g,SequenceI s) ;
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51 public void addGroup(SequenceGroup sg) ;
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52 public void deleteGroup(SequenceGroup g) ;
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53 public Vector getGroups();
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54 public void deleteAllGroups();
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56 public void addSuperGroup(SuperGroup sg);
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57 public void removeSuperGroup(SuperGroup sg);
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58 public SuperGroup getSuperGroup(SequenceGroup sg);
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61 public void sortGroups() ;
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62 public void sortByPID(SequenceI s) ;
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63 public void sortByID() ;
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66 public void addAnnotation(AlignmentAnnotation aa);
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67 public void deleteAnnotation(AlignmentAnnotation aa);
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68 public AlignmentAnnotation [] getAlignmentAnnotation();
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70 public void setGapCharacter(char gc);
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71 public char getGapCharacter();
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73 public Vector getAAFrequency();
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