Alignable (biojava 5.3.0 API)

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All Known Implementing Classes:

StrCompAlignment
```
public interface Alignable
```

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`AligMatEl[][]`	`getAligMat()`
`int`	`getCols()`
`float`	`getGapExtCol()`
`float`	`getGapExtRow()`
`float`	`getGapOpenCol()`
`float`	`getGapOpenRow()`
`IndexPair[]`	`getPath()`
`int`	`getPathSize()`
`int`	`getRows()`
`float`	`getScore()`
`void`	`setAligMat(AligMatEl[][] alignmentMatrix)`
`void`	`setGapExtCol(float penalty)`
`void`	`setGapExtRow(float penalty)`
`void`	`setGapOpenCol(float penalty)`
`void`	`setGapOpenRow(float penalty)`
`void`	`setPath(IndexPair[] path)`
`void`	`setPathSize(int pathSize)`
`void`	`setScore(float score)`

Method Detail

getRows
```
int getRows()
```

getCols
```
int getCols()
```

getAligMat
```
AligMatEl[][] getAligMat()
```

setAligMat

void setAligMat(AligMatEl[][] alignmentMatrix)

getGapExtCol
```
float getGapExtCol()
```

setGapExtCol
```
void setGapExtCol(float penalty)
```

getGapExtRow
```
float getGapExtRow()
```

setGapExtRow
```
void setGapExtRow(float penalty)
```

getGapOpenCol
```
float getGapOpenCol()
```

setGapOpenCol
```
void setGapOpenCol(float penalty)
```

getGapOpenRow
```
float getGapOpenRow()
```

setGapOpenRow
```
void setGapOpenRow(float penalty)
```

setScore
```
void setScore(float score)
```

getScore
```
float getScore()
```

getPathSize
```
int getPathSize()
```

setPathSize
```
void setPathSize(int pathSize)
```

setPath
```
void setPath(IndexPair[] path)
```

getPath
```
IndexPair[] getPath()
```

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