| /trunk/PhyloWidget/src/org/phylowidget/UsefulConstants.java r152 | /trunk/PhyloWidget/src/org/phylowidget/UsefulConstants.java r156 | ||
| 1 | package org.phylowidget; | 1 | package org.phylowidget; |
|---|---|---|---|
| 2 | 2 | ||
| 3 | public interface UsefulConstants | 3 | public interface UsefulConstants |
| 4 | { | 4 | { |
| 5 | /** | 5 | /** |
| 6 | * NHX Annotation variables. (defined at http://www.phylosoft.org/forester/NHX.html). | 6 | * NHX Annotation variables. (defined at http://www.phylosoft.org/forester/NHX.html). |
| 7 | */ | 7 | */ |
| 8 | public static final String GENE_NAME = "GN"; | 8 | public static final String GENE_NAME = "GN"; |
| 9 | public static final String BOOTSTRAP = "B"; | 9 | public static final String BOOTSTRAP = "B"; |
| 10 | public static final String DUPLICATION = "D"; | 10 | public static final String DUPLICATION = "D"; |
| 11 | public static final String SPECIES_NAME = "S"; | 11 | public static final String SPECIES_NAME = "S"; |
| 12 | public static final String TAXON_ID = "T"; | 12 | public static final String TAXON_ID = "T"; |
| 13 | // Some of these are commented out; they are part of the NHX definition, but PW doesn't use them. | 13 | // Some of these are commented out; they are part of the NHX definition, but PW doesn't use them. |
| 14 | // public static final String ACCESSION = "AC"; | 14 | // public static final String ACCESSION = "AC"; |
| 15 | // public static final String NODE_IDENTIFIER = "ND"; | 15 | // public static final String NODE_IDENTIFIER = "ND"; |
| 16 | // public static final String EC_NUMBER = "EC"; | 16 | // public static final String EC_NUMBER = "EC"; |
| 17 | // public static final String FUNCTION = "FU"; | 17 | // public static final String FUNCTION = "FU"; |
| 18 | // public static final String DOMAIN_STRUCTURE = "DS"; | 18 | // public static final String DOMAIN_STRUCTURE = "DS"; |
| 19 | // public static final String BRANCH_WIDTH = "W"; // TODO: Implement this, it should be easy! | 19 | // public static final String BRANCH_WIDTH = "W"; // TODO: Implement this, it should be easy! |
| 20 | // public static final String COLOR = "C"; // This is the original color annotation, but PW instead uses the more flexible 3-color annotation seen below. | 20 | // public static final String COLOR = "C"; // This is the original color annotation, but PW instead uses the more flexible 3-color annotation seen below. |
| 21 | // public static final String COLLAPSE_NODE = "CO"; // TODO: Implement this, even though it may be tough... | 21 | // public static final String COLLAPSE_NODE = "CO"; // TODO: Implement this, even though it may be tough... |
| 22 | // public static final String EXTRA_BRANCH_DATA = "XB"; | 22 | // public static final String EXTRA_BRANCH_DATA = "XB"; |
| 23 | // public static final String EXTRA_NODE_DATA = "XN"; | 23 | // public static final String EXTRA_NODE_DATA = "XN"; |
| 24 | // public static final String ORTHOLOGOUS_TO = "O"; | 24 | // public static final String ORTHOLOGOUS_TO = "O"; |
| 25 | // public static final String SUBTREE_NEIGHBORS = "SN"; | 25 | // public static final String SUBTREE_NEIGHBORS = "SN"; |
| 26 | // public static final String SUPER_ORTHOLOGOUS = "SO"; | 26 | // public static final String SUPER_ORTHOLOGOUS = "SO"; |
| 27 | 27 | ||
| 28 | 28 | ||
| 29 | // Below are some of our own juicy extras, stacked on top of the plain vanilla NHX. | 29 | // Below are some of our own juicy extras, stacked on top of the plain vanilla NHX. |
| 30 | public static final String IMG_TAG = "IMG"; // a URL to an image that will be displayed. | 30 | public static final String IMG_TAG = "IMG"; // a URL to an image that will be displayed. |
| 31 | public static final String OLD_IMG_TAG = "OLD_IMG"; // Used for internal caching purposes by PhyloWidget. | 31 | public static final String OLD_IMG_TAG = "OLD_IMG"; // Used for internal caching purposes by PhyloWidget. |
| 32 | 32 | ||
| 33 | public static final String CIGAR = "CIGAR"; // Cigar line, for gene tree alignments. | ||
| 34 | |||
| 33 | public static final String LABEL_COLOR = "LCOL"; // Color of a node's label | 35 | public static final String LABEL_COLOR = "LCOL"; // Color of a node's label |
| 34 | public static final String NODE_COLOR = "NCOL"; // Color of a node's dot marker | 36 | public static final String NODE_COLOR = "NCOL"; // Color of a node's dot marker |
| 35 | public static final String BRANCH_COLOR = "BCOL"; // Color of a node's branch (the branch leading to its parent) | 37 | public static final String BRANCH_COLOR = "BCOL"; // Color of a node's branch (the branch leading to its parent) |
| 38 | public static final String ALIGNMENT_COLOR = "ALNCOL"; // Color of a node's branch (the branch leading to its parent) | ||
| 36 | // NB: The values of the color annotations should be in R,G,B format, either with or without parentheses (your choice!) | 39 | // NB: The values of the color annotations should be in R,G,B format, either with or without parentheses (your choice!) |
| 37 | // [Alternatively, if you specify a single integer value, it will be interpreted as a single grayscale value] | 40 | // [Alternatively, if you specify a single integer value, it will be interpreted as a single grayscale value] |
| 38 | // NB: The above color annotations take precedence over any other auto-coloring that is usually done. | 41 | // NB: The above color annotations take precedence over any other auto-coloring that is usually done. |
| 39 | public static final String LABEL_SIZE = "LSZ"; // Multiplier for label text size. | 42 | public static final String LABEL_SIZE = "LSZ"; // Multiplier for label text size. |
| 40 | public static final String NODE_SIZE = "NSZ"; // Multiplier for node marker size. | 43 | public static final String NODE_SIZE = "NSZ"; // Multiplier for node marker size. |
| 44 | public static final String NODE_SHAPE = "NSH"; | ||
| 41 | public static final String BRANCH_SIZE = "BSZ"; // Multiplier for branch thickness size. | 45 | public static final String BRANCH_SIZE = "BSZ"; // Multiplier for branch thickness size. |
| 42 | public static final String IMAGE_SIZE = "ISZ"; // Multiplier for photo size. | 46 | public static final String IMAGE_SIZE = "ISZ"; // Multiplier for photo size. |
| 47 | public static final String CIGAR_SIZE = "ALNSZ"; // Multiplier for photo size. | ||
| 43 | public static final String LABEL_ALWAYSSHOW = "PW_ALWAYS"; // Pretty hacky, but this is a tag to make sure a label is ALWAYS shown, no matter what. | 48 | public static final String LABEL_ALWAYSSHOW = "PW_ALWAYS"; // Pretty hacky, but this is a tag to make sure a label is ALWAYS shown, no matter what. |
| 44 | public static final String Z_ORDER = "PW_Z"; // Another hack: specify the z-order of the node, to be used in combination with ALWAYSSHOW. | 49 | public static final String Z_ORDER = "PW_Z"; // Another hack: specify the z-order of the node, to be used in combination with ALWAYSSHOW. |
| 45 | } | 50 | } |
